From dalke at dalkescientific.com Fri Jun 3 14:50:47 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 3 Jun 2005 12:50:47 -0600 Subject: [DAS2] structure DAS Message-ID: I've been thinking more about the general idea of a structure DAS. I think it would be good to have someone with more recent (and better) structure knowledge than I do. This may be the woman from RCSB mentioned yesterday. Another idea is Steven Brenner. There are two main ways to think about proteins: sequence and conformation. The sequence model is similar to that used for DNA. Sequences have residues arranged in a line, with positions numbered by position. The biggest database for this is SWISS-PROT. Here's an example of features FT DOMAIN 583 920 HECT. FT REGION 515 571 PABP-like. FT COMPBIAS 108 119 Asp/Glu-rich (acidic). FT COMPBIAS 158 181 Pro-rich. FT COMPBIAS 451 470 Arg/Glu-rich (mixed charge). FT COMPBIAS 479 488 Arg/Asp-rich (mixed charge). FT COMPBIAS 610 621 Asp/Glu-rich (acidic). FT COMPBIAS 858 878 Pro-rich. FT ACT_SITE 889 889 Glycyl thioester intermediate (By FT similarity). These are feature types, start/end position, and a description. I imagine there is an ontology for these but I haven't been following that work. Structure is more complicated. The biggest data source for this is the PDB. Things to worry about: * a PDB record may contain aggregates of protein, DNA, lipids, waters, ions, ligands, post-translational modifications and other bits and pieces. * the sequence listed for a chain may be different than found from crystallography. * residue numbers in the structure may not be consecutive. Eg, in a chain the residue ids may be -2, -1, 1, 2A, 2B, 2C. The numbering is often done to preserve residue identifiers across homologous structures. * some features are at the atomic level and not feature level. For that matter, some people like things like "center of ring" but I think we can ignore those. Others like "binding pocket" but there's no good way to specify that. * some residues have "alternate" conformations, eg, a side chain that's believed to have two common orientations. I don't think we need to worry about this. * NMR structures (and others) may have multiple models. I think we don't need to worry about this. All programs I know of handle these as alternate conformations and have no way to say a given feature is on only one of those conformations. * some features may be over several regions of a protein, or across several different chains. Eg, a disulphide bond between two different proteins or an indicator of a beta barrel composed of multiple proteins * strange things, like a protein covalently bonded to a piece of DNA. Those chemists are so whacky! Here's a picture of one done in my old group http://www.ks.uiuc.edu/Research/pro_DNA/hmgd/SDNA_t.gif from http://www.ks.uiuc.edu/Research/pro_DNA/hmgd/ I think it's okay to linearize these. * crystal structures and symmetries. One example that comes to mind is the virus structure I worked on where a beta sheet went from one protein chain on the given protomer to another protein chain on the next protomer around the 5-fold symmetry access. But the structure record only contains a single protomer. I don't think we need to worry about this because to the best of my knowledge that information is not available in any database; it's extracted by humans reading the comments and associated papers. Beyond the technical details, Who are the test users? What's the reference platform? Should there even be one? There's a boatload of 3d structure viewers. A decade ago Steven Brenner proposed a generic format for selection + annotation information. Perhaps that's a better path? Is writeback needed? Andrew dalke at dalkescientific.com From th at sanger.ac.uk Fri Jun 3 15:31:20 2005 From: th at sanger.ac.uk (Tim Hubbard) Date: Fri, 3 Jun 2005 20:31:20 +0100 Subject: [DAS2] structure DAS In-Reply-To: References: Message-ID: Hi Andrew, We already have a DAS1 enabled structure browser (SPICE - java webstart based on JMol) as part of the efamily project - see here: http://www.efamily.org.uk/software/dasclients/spice/ This gets structure information from a reference DAS1 server that has been extended with a 'structure' command (spits out 3D coordinates as well as sequence). There are various plugins for this server that will server coordinate sets from raw PDB files, a replicated oracle instance of MSD and structures contained in SRS. SPICE can display features from DAS servers on either PDBRESNUM coordinate or UNIPROT coordinate systems. There's an DAS alignment service (another DAS1 extension that we've implemented) that provides the mapping between the two coordinate systems. By default, SPICE gets information about available DAS servers from a DAS server registry that we have setup and are starting to use seriously. The following is the interface for browsing lists, but the registry itself is a webservice that can be called and queried from clients http://das.sanger.ac.uk/registry/listServices.jsp (select name 'UniProt' or 'PDBresnum' to get lists of what services have been registered with this. Both the efamily and Biosapiens projects are using this) This doesn't of course address true 3D DAS (DAS servers that provide 3D points or surfaces wrt to 3D structures) but it does allow us to map sequence features onto structure easily and we'll be building on it. SPICE and the associated DAS extensions have been implemented by Andreas Prlic - with some help from Thomas Down, the developer of Dazzle and others at Sanger. I'm sure they will chime in with details to questions about this. Tim At 12:50 pm -0600 3/6/05, Andrew Dalke wrote: >I've been thinking more about the general idea of a structure DAS. > >I think it would be good to have someone with more recent >(and better) structure knowledge than I do. This may be >the woman from RCSB mentioned yesterday. Another idea is >Steven Brenner. > >There are two main ways to think about proteins: sequence >and conformation. > >The sequence model is similar to that used for DNA. >Sequences have residues arranged in a line, with positions >numbered by position. > >The biggest database for this is SWISS-PROT. Here's >an example of features > >FT DOMAIN 583 920 HECT. >FT REGION 515 571 PABP-like. >FT COMPBIAS 108 119 Asp/Glu-rich (acidic). >FT COMPBIAS 158 181 Pro-rich. >FT COMPBIAS 451 470 Arg/Glu-rich (mixed charge). >FT COMPBIAS 479 488 Arg/Asp-rich (mixed charge). >FT COMPBIAS 610 621 Asp/Glu-rich (acidic). >FT COMPBIAS 858 878 Pro-rich. >FT ACT_SITE 889 889 Glycyl thioester intermediate (By >FT similarity). > >These are feature types, start/end position, and a description. >I imagine there is an ontology for these but I haven't been >following that work. > > >Structure is more complicated. The biggest data source >for this is the PDB. Things to worry about: > > * a PDB record may contain aggregates of protein, DNA, lipids, >waters, ions, ligands, post-translational modifications and >other bits and pieces. > > * the sequence listed for a chain may be different than >found from crystallography. > > * residue numbers in the structure may not be consecutive. Eg, >in a chain the residue ids may be -2, -1, 1, 2A, 2B, 2C. The >numbering is often done to preserve residue identifiers across >homologous structures. > > * some features are at the atomic level and not feature level. >For that matter, some people like things like "center of ring" >but I think we can ignore those. Others like "binding pocket" >but there's no good way to specify that. > > * some residues have "alternate" conformations, eg, a side >chain that's believed to have two common orientations. I >don't think we need to worry about this. > > * NMR structures (and others) may have multiple models. >I think we don't need to worry about this. All programs I >know of handle these as alternate conformations and have >no way to say a given feature is on only one of those >conformations. > > * some features may be over several regions of a protein, >or across several different chains. Eg, a disulphide bond >between two different proteins or an indicator of a beta >barrel composed of multiple proteins > > * strange things, like a protein covalently bonded to a >piece of DNA. Those chemists are so whacky! Here's a >picture of one done in my old group > http://www.ks.uiuc.edu/Research/pro_DNA/hmgd/SDNA_t.gif >from > http://www.ks.uiuc.edu/Research/pro_DNA/hmgd/ >I think it's okay to linearize these. > > * crystal structures and symmetries. One example that >comes to mind is the virus structure I worked on where >a beta sheet went from one protein chain on the given >protomer to another protein chain on the next protomer >around the 5-fold symmetry access. But the structure >record only contains a single protomer. I don't think >we need to worry about this because to the best of >my knowledge that information is not available in >any database; it's extracted by humans reading the >comments and associated papers. > > >Beyond the technical details, > > Who are the test users? > > What's the reference platform? Should there even be one? >There's a boatload of 3d structure viewers. A decade ago >Steven Brenner proposed a generic format for selection + >annotation information. Perhaps that's a better path? > > Is writeback needed? > > Andrew > dalke at dalkescientific.com > >_______________________________________________ >DAS2 mailing list >DAS2 at portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/das2 -- ---------------------------------------------------------------------------- Dr Tim Hubbard email: th at sanger.ac.uk Head of Human Genome Analysis Tel (direct): +44 1223 496886 Wellcome Trust Sanger Institute Tel (switch): +44 1223 834244 Wellcome Trust Genome Campus, Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. UK. URL: http://www.sanger.ac.uk/Users/th ---------------------------------------------------------------------------- From dalke at dalkescientific.com Tue Jun 7 03:32:14 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 7 Jun 2005 01:32:14 -0600 Subject: [DAS2] early dasypus output Message-ID: While at this point its mostly readable only by me, here's an example of the current dasypus validation. As you can see, there are many things to fix in both the current server and the spec. Andrew [Andrew-Dalkes-Computer:~/cvses/dasypus/dasypus] dalke% python dasypus.py ========> client.sources <=============== ERROR Unknown content-type 'text/x-das-source+xml' for service 'sources' WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: Fixing DAS namespace {http://www.biodas.org/ns/das/2.00}SOURCES; should be {http://www.biodas.org/ns/das/genome/2.00}SOURCES WARNING: Fixing base of http://das.biopackages.net:0/das; should be http://das.biopackages.net/das/genome/ Comparing sources with single source ========> client.source <=============== ERROR Unknown content-type 'text/das-source+xml' for service 'source' WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: Fixing DAS namespace {http://www.biodas.org/ns/das/2.00}SOURCES; should be {http://www.biodas.org/ns/das/genome/2.00}SOURCES Different: taxon: 'FIXME' != 'http://www.ncbi.nlm.nih.gov/taxon-browser?id=FIXME' ========> client.detailed_source <=============== ERROR Unknown content-type 'text/x-das-source-details+xml' for service 'detailed_source' WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: VERSION tag not closed WARNING: Fixing DAS namespace {http://www.biodas.org/ns/das/2.00}SOURCE; should be {http://www.biodas.org/ns/das/genome/2.00}SOURCE WARNING: Detailed SOURCE description=='blahblahblah' WARNING: Detailed SOURCE VERSION[0] description=='blahblahblah' ERROR Detailed SOURCE VERSION[0] created=='FIXME, a timestamp' not ISO date ERROR Detailed SOURCE VERSION[0] modified=='FIXME, a timestamp' not ISO date different id 'http://das.biopackages.net/das/genome/chado/chado-Hsa-17' != 'chado' types_url http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing WARNING: TYPES TYPE[1] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[1] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[1] source=="whatever" WARNING: TYPES TYPE[1] uses xml:base; add to the DAS/2 spec ERROR server gives 505 error with '%s'. Removing. WARNING: TYPES TYPE[2] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[2] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[2] source=="whatever" WARNING: TYPES TYPE[2] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[2] id=="SO:five_prime_UTR" is not a valid relative URL; fixing WARNING: TYPES TYPE[3] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[3] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[3] source=="whatever" WARNING: TYPES TYPE[3] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[3] id=="SO:gene_part" is not a valid relative URL; fixing WARNING: TYPES TYPE[4] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[4] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[4] source=="whatever" WARNING: TYPES TYPE[4] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[4] id=="SO:located_sequence_feature" is not a valid relative URL; fixing WARNING: TYPES TYPE[5] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[5] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[5] source=="whatever" WARNING: TYPES TYPE[5] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[5] id=="SO:mature_peptide" is not a valid relative URL; fixing WARNING: TYPES TYPE[6] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[6] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[6] source=="whatever" WARNING: TYPES TYPE[6] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[6] id=="SO:mRNA" is not a valid relative URL; fixing WARNING: TYPES TYPE[7] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[7] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[7] source=="whatever" WARNING: TYPES TYPE[7] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[7] id=="SO:PCR_product" is not a valid relative URL; fixing WARNING: TYPES TYPE[8] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[8] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[8] source=="whatever" WARNING: TYPES TYPE[8] uses xml:base; add to the DAS/2 spec ERROR server gives 505 error with '%s'. Removing. WARNING: TYPES TYPE[9] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[9] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[9] source=="whatever" WARNING: TYPES TYPE[9] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[9] id=="SO:polypeptide" is not a valid relative URL; fixing WARNING: TYPES TYPE[10] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[10] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[10] source=="whatever" WARNING: TYPES TYPE[10] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[10] id=="SO:primary_transcript" is not a valid relative URL; fixing WARNING: TYPES TYPE[11] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[11] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[11] source=="whatever" WARNING: TYPES TYPE[11] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[11] id=="SO:processed_transcript" is not a valid relative URL; fixing WARNING: TYPES TYPE[12] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[12] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[12] source=="whatever" WARNING: TYPES TYPE[12] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[12] id=="SO:reagent" is not a valid relative URL; fixing WARNING: TYPES TYPE[13] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[13] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[13] source=="whatever" WARNING: TYPES TYPE[13] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[13] id=="SO:region" is not a valid relative URL; fixing WARNING: TYPES TYPE[14] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[14] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[14] source=="whatever" WARNING: TYPES TYPE[14] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[14] id=="SO:SNP" is not a valid relative URL; fixing WARNING: TYPES TYPE[15] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[15] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[15] source=="whatever" WARNING: TYPES TYPE[15] uses xml:base; add to the DAS/2 spec ERROR server gives 505 error with '%s'. Removing. WARNING: TYPES TYPE[16] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[16] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[16] source=="whatever" WARNING: TYPES TYPE[16] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[16] id=="SO:three_prime_UTR" is not a valid relative URL; fixing WARNING: TYPES TYPE[17] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[17] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[17] source=="whatever" WARNING: TYPES TYPE[17] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[17] id=="SO:transcript" is not a valid relative URL; fixing WARNING: TYPES TYPE[18] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[18] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[18] source=="whatever" WARNING: TYPES TYPE[18] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[18] id=="SO:UTR" is not a valid relative URL; fixing WARNING: TYPES TYPE[19] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[19] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[19] source=="whatever" WARNING: TYPES TYPE[19] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[19] id=="SO:protein" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:CDS WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: five_prime_UTR WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:five_prime_UTR" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: gene_part WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:gene_part" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: located_sequence_feature WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:located_sequence_feature" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: mature_peptide WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:mature_peptide" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:mRNA WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:mRNA" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: PCR_product WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:PCR_product" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: polypeptide WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:polypeptide" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: primary_transcript WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:primary_transcript" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: processed_transcript WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:processed_transcript" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: reagent WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:reagent" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:region WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:region" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:SNP WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:SNP" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: three_prime_UTR WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:three_prime_UTR" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: transcript WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:transcript" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:UTR WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:UTR" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: protein WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:protein" is not a valid relative URL; fixing [Andrew-Dalkes-Computer:~/cvses/dasypus/dasypus] dalke% Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Tue Jun 7 03:38:39 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 7 Jun 2005 01:38:39 -0600 Subject: [DAS2] squid proxy Message-ID: <2af3af7d3d958611b8d282682efd584b@dalkescientific.com> P.S. Development was much more fun once I set up a Squid proxy for the dev. server and forced it to cache everything for up to a day. Besides getting rid of the network overhead, some of the server responses (like 'type') take a noticeable time. In doing that I found a bug in dasypus. The HTTP request object changes when using a server, so http://www.biodas.org/blah becomes (in effect) http://proxy/http://www.biodas.org/blah Some of my fixups and tests are server-specific and I didn't expect the request server name to change from underneath me. Andrew dalke at dalkescientific.com From allenday at ucla.edu Tue Jun 7 03:53:44 2005 From: allenday at ucla.edu (Allen Day) Date: Tue, 7 Jun 2005 00:53:44 -0700 (PDT) Subject: [DAS2] early dasypus output In-Reply-To: References: Message-ID: This is very helpful. I'm updating the test server tonight, have a look again in a few hours. -Allen On Tue, 7 Jun 2005, Andrew Dalke wrote: > While at this point its mostly readable only by me, here's an example > of the current dasypus validation. > > As you can see, there are many things to fix in both the current > server and the spec. > > Andrew > > > [Andrew-Dalkes-Computer:~/cvses/dasypus/dasypus] dalke% python > dasypus.py > ========> client.sources <=============== > > > ERROR Unknown content-type 'text/x-das-source+xml' for service 'sources' > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: Fixing DAS namespace > {http://www.biodas.org/ns/das/2.00}SOURCES; should be > {http://www.biodas.org/ns/das/genome/2.00}SOURCES > WARNING: Fixing base of http://das.biopackages.net:0/das; should be > http://das.biopackages.net/das/genome/ > Comparing sources with single source > ========> client.source <=============== > > > ERROR Unknown content-type 'text/das-source+xml' for service 'source' > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: Fixing DAS namespace > {http://www.biodas.org/ns/das/2.00}SOURCES; should be > {http://www.biodas.org/ns/das/genome/2.00}SOURCES > Different: > taxon: 'FIXME' != 'http://www.ncbi.nlm.nih.gov/taxon-browser?id=FIXME' > ========> client.detailed_source <=============== > > > ERROR Unknown content-type 'text/x-das-source-details+xml' for service > 'detailed_source' > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: VERSION tag not closed > WARNING: Fixing DAS namespace > {http://www.biodas.org/ns/das/2.00}SOURCE; should be > {http://www.biodas.org/ns/das/genome/2.00}SOURCE > WARNING: Detailed SOURCE description=='blahblahblah' > WARNING: Detailed SOURCE VERSION[0] description=='blahblahblah' > ERROR Detailed SOURCE VERSION[0] created=='FIXME, a timestamp' not ISO > date > ERROR Detailed SOURCE VERSION[0] modified=='FIXME, a timestamp' not ISO > date > different id > 'http://das.biopackages.net/das/genome/chado/chado-Hsa-17' != 'chado' > types_url http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing > WARNING: TYPES TYPE[1] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[1] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[1] source=="whatever" > WARNING: TYPES TYPE[1] uses xml:base; add to the DAS/2 spec > ERROR server gives 505 error with '%s'. Removing. > WARNING: TYPES TYPE[2] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[2] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[2] source=="whatever" > WARNING: TYPES TYPE[2] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[2] id=="SO:five_prime_UTR" is not a valid relative > URL; fixing > WARNING: TYPES TYPE[3] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[3] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[3] source=="whatever" > WARNING: TYPES TYPE[3] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[3] id=="SO:gene_part" is not a valid relative URL; > fixing > WARNING: TYPES TYPE[4] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[4] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[4] source=="whatever" > WARNING: TYPES TYPE[4] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[4] id=="SO:located_sequence_feature" is not a valid > relative URL; fixing > WARNING: TYPES TYPE[5] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[5] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[5] source=="whatever" > WARNING: TYPES TYPE[5] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[5] id=="SO:mature_peptide" is not a valid relative > URL; fixing > WARNING: TYPES TYPE[6] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[6] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[6] source=="whatever" > WARNING: TYPES TYPE[6] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[6] id=="SO:mRNA" is not a valid relative URL; fixing > WARNING: TYPES TYPE[7] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[7] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[7] source=="whatever" > WARNING: TYPES TYPE[7] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[7] id=="SO:PCR_product" is not a valid relative URL; > fixing > WARNING: TYPES TYPE[8] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[8] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[8] source=="whatever" > WARNING: TYPES TYPE[8] uses xml:base; add to the DAS/2 spec > ERROR server gives 505 error with '%s'. Removing. > WARNING: TYPES TYPE[9] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[9] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[9] source=="whatever" > WARNING: TYPES TYPE[9] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[9] id=="SO:polypeptide" is not a valid relative URL; > fixing > WARNING: TYPES TYPE[10] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[10] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[10] source=="whatever" > WARNING: TYPES TYPE[10] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[10] id=="SO:primary_transcript" is not a valid > relative URL; fixing > WARNING: TYPES TYPE[11] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[11] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[11] source=="whatever" > WARNING: TYPES TYPE[11] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[11] id=="SO:processed_transcript" is not a valid > relative URL; fixing > WARNING: TYPES TYPE[12] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[12] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[12] source=="whatever" > WARNING: TYPES TYPE[12] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[12] id=="SO:reagent" is not a valid relative URL; > fixing > WARNING: TYPES TYPE[13] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[13] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[13] source=="whatever" > WARNING: TYPES TYPE[13] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[13] id=="SO:region" is not a valid relative URL; fixing > WARNING: TYPES TYPE[14] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[14] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[14] source=="whatever" > WARNING: TYPES TYPE[14] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[14] id=="SO:SNP" is not a valid relative URL; fixing > WARNING: TYPES TYPE[15] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[15] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[15] source=="whatever" > WARNING: TYPES TYPE[15] uses xml:base; add to the DAS/2 spec > ERROR server gives 505 error with '%s'. Removing. > WARNING: TYPES TYPE[16] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[16] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[16] source=="whatever" > WARNING: TYPES TYPE[16] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[16] id=="SO:three_prime_UTR" is not a valid relative > URL; fixing > WARNING: TYPES TYPE[17] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[17] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[17] source=="whatever" > WARNING: TYPES TYPE[17] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[17] id=="SO:transcript" is not a valid relative URL; > fixing > WARNING: TYPES TYPE[18] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[18] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[18] source=="whatever" > WARNING: TYPES TYPE[18] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[18] id=="SO:UTR" is not a valid relative URL; fixing > WARNING: TYPES TYPE[19] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[19] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[19] source=="whatever" > WARNING: TYPES TYPE[19] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[19] id=="SO:protein" is not a valid relative URL; > fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:CDS > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > five_prime_UTR > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:five_prime_UTR" is not a valid relative > URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > gene_part > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:gene_part" is not a valid relative URL; > fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > located_sequence_feature > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:located_sequence_feature" is not a valid > relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > mature_peptide > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:mature_peptide" is not a valid relative > URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:mRNA > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:mRNA" is not a valid relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > PCR_product > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:PCR_product" is not a valid relative URL; > fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > polypeptide > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:polypeptide" is not a valid relative URL; > fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > primary_transcript > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:primary_transcript" is not a valid relative > URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > processed_transcript > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:processed_transcript" is not a valid > relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > reagent > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:reagent" is not a valid relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:region > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:region" is not a valid relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:SNP > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:SNP" is not a valid relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > three_prime_UTR > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:three_prime_UTR" is not a valid relative > URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > transcript > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:transcript" is not a valid relative URL; > fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:UTR > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:UTR" is not a valid relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > protein > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:protein" is not a valid relative URL; fixing > [Andrew-Dalkes-Computer:~/cvses/dasypus/dasypus] dalke% > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 > From allenday at ucla.edu Tue Jun 7 04:06:43 2005 From: allenday at ucla.edu (Allen Day) Date: Tue, 7 Jun 2005 01:06:43 -0700 (PDT) Subject: [DAS2] early dasypus output In-Reply-To: References: Message-ID: Okay, new code is up. I believe I have fixed the bug from below > > ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing as well as > > WARNING: VERSION tag not closed > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > {http://www.biodas.org/ns/das/2.00}SOURCES; should be -Allen On Tue, 7 Jun 2005, Allen Day wrote: > This is very helpful. I'm updating the test server tonight, have a look > again in a few hours. > > -Allen > > On Tue, 7 Jun 2005, Andrew Dalke wrote: > > > While at this point its mostly readable only by me, here's an example > > of the current dasypus validation. > > > > As you can see, there are many things to fix in both the current > > server and the spec. > > > > Andrew > > > > > > [Andrew-Dalkes-Computer:~/cvses/dasypus/dasypus] dalke% python > > dasypus.py > > ========> client.sources <=============== > > > > > > ERROR Unknown content-type 'text/x-das-source+xml' for service 'sources' > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: Fixing DAS namespace > > {http://www.biodas.org/ns/das/2.00}SOURCES; should be > > {http://www.biodas.org/ns/das/genome/2.00}SOURCES > > WARNING: Fixing base of http://das.biopackages.net:0/das; should be > > http://das.biopackages.net/das/genome/ > > Comparing sources with single source > > ========> client.source <=============== > > > > > > ERROR Unknown content-type 'text/das-source+xml' for service 'source' > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: Fixing DAS namespace > > {http://www.biodas.org/ns/das/2.00}SOURCES; should be > > {http://www.biodas.org/ns/das/genome/2.00}SOURCES > > Different: > > taxon: 'FIXME' != 'http://www.ncbi.nlm.nih.gov/taxon-browser?id=FIXME' > > ========> client.detailed_source <=============== > > > > > > ERROR Unknown content-type 'text/x-das-source-details+xml' for service > > 'detailed_source' > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: VERSION tag not closed > > WARNING: Fixing DAS namespace > > {http://www.biodas.org/ns/das/2.00}SOURCE; should be > > {http://www.biodas.org/ns/das/genome/2.00}SOURCE > > WARNING: Detailed SOURCE description=='blahblahblah' > > WARNING: Detailed SOURCE VERSION[0] description=='blahblahblah' > > ERROR Detailed SOURCE VERSION[0] created=='FIXME, a timestamp' not ISO > > date > > ERROR Detailed SOURCE VERSION[0] modified=='FIXME, a timestamp' not ISO > > date > > different id > > 'http://das.biopackages.net/das/genome/chado/chado-Hsa-17' != 'chado' > > types_url http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing > > WARNING: TYPES TYPE[1] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[1] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[1] source=="whatever" > > WARNING: TYPES TYPE[1] uses xml:base; add to the DAS/2 spec > > ERROR server gives 505 error with '%s'. Removing. > > WARNING: TYPES TYPE[2] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[2] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[2] source=="whatever" > > WARNING: TYPES TYPE[2] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[2] id=="SO:five_prime_UTR" is not a valid relative > > URL; fixing > > WARNING: TYPES TYPE[3] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[3] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[3] source=="whatever" > > WARNING: TYPES TYPE[3] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[3] id=="SO:gene_part" is not a valid relative URL; > > fixing > > WARNING: TYPES TYPE[4] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[4] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[4] source=="whatever" > > WARNING: TYPES TYPE[4] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[4] id=="SO:located_sequence_feature" is not a valid > > relative URL; fixing > > WARNING: TYPES TYPE[5] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[5] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[5] source=="whatever" > > WARNING: TYPES TYPE[5] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[5] id=="SO:mature_peptide" is not a valid relative > > URL; fixing > > WARNING: TYPES TYPE[6] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[6] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[6] source=="whatever" > > WARNING: TYPES TYPE[6] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[6] id=="SO:mRNA" is not a valid relative URL; fixing > > WARNING: TYPES TYPE[7] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[7] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[7] source=="whatever" > > WARNING: TYPES TYPE[7] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[7] id=="SO:PCR_product" is not a valid relative URL; > > fixing > > WARNING: TYPES TYPE[8] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[8] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[8] source=="whatever" > > WARNING: TYPES TYPE[8] uses xml:base; add to the DAS/2 spec > > ERROR server gives 505 error with '%s'. Removing. > > WARNING: TYPES TYPE[9] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[9] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[9] source=="whatever" > > WARNING: TYPES TYPE[9] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[9] id=="SO:polypeptide" is not a valid relative URL; > > fixing > > WARNING: TYPES TYPE[10] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[10] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[10] source=="whatever" > > WARNING: TYPES TYPE[10] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[10] id=="SO:primary_transcript" is not a valid > > relative URL; fixing > > WARNING: TYPES TYPE[11] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[11] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[11] source=="whatever" > > WARNING: TYPES TYPE[11] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[11] id=="SO:processed_transcript" is not a valid > > relative URL; fixing > > WARNING: TYPES TYPE[12] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[12] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[12] source=="whatever" > > WARNING: TYPES TYPE[12] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[12] id=="SO:reagent" is not a valid relative URL; > > fixing > > WARNING: TYPES TYPE[13] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[13] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[13] source=="whatever" > > WARNING: TYPES TYPE[13] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[13] id=="SO:region" is not a valid relative URL; fixing > > WARNING: TYPES TYPE[14] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[14] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[14] source=="whatever" > > WARNING: TYPES TYPE[14] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[14] id=="SO:SNP" is not a valid relative URL; fixing > > WARNING: TYPES TYPE[15] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[15] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[15] source=="whatever" > > WARNING: TYPES TYPE[15] uses xml:base; add to the DAS/2 spec > > ERROR server gives 505 error with '%s'. Removing. > > WARNING: TYPES TYPE[16] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[16] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[16] source=="whatever" > > WARNING: TYPES TYPE[16] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[16] id=="SO:three_prime_UTR" is not a valid relative > > URL; fixing > > WARNING: TYPES TYPE[17] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[17] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[17] source=="whatever" > > WARNING: TYPES TYPE[17] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[17] id=="SO:transcript" is not a valid relative URL; > > fixing > > WARNING: TYPES TYPE[18] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[18] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[18] source=="whatever" > > WARNING: TYPES TYPE[18] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[18] id=="SO:UTR" is not a valid relative URL; fixing > > WARNING: TYPES TYPE[19] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[19] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[19] source=="whatever" > > WARNING: TYPES TYPE[19] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[19] id=="SO:protein" is not a valid relative URL; > > fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:CDS > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > five_prime_UTR > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:five_prime_UTR" is not a valid relative > > URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > gene_part > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:gene_part" is not a valid relative URL; > > fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > located_sequence_feature > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:located_sequence_feature" is not a valid > > relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > mature_peptide > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:mature_peptide" is not a valid relative > > URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:mRNA > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:mRNA" is not a valid relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > PCR_product > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:PCR_product" is not a valid relative URL; > > fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > polypeptide > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:polypeptide" is not a valid relative URL; > > fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > primary_transcript > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:primary_transcript" is not a valid relative > > URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > processed_transcript > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:processed_transcript" is not a valid > > relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > reagent > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:reagent" is not a valid relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:region > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:region" is not a valid relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:SNP > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:SNP" is not a valid relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > three_prime_UTR > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:three_prime_UTR" is not a valid relative > > URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > transcript > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:transcript" is not a valid relative URL; > > fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:UTR > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:UTR" is not a valid relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > protein > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:protein" is not a valid relative URL; fixing > > [Andrew-Dalkes-Computer:~/cvses/dasypus/dasypus] dalke% > > > > Andrew > > dalke at dalkescientific.com > > > > _______________________________________________ > > DAS2 mailing list > > DAS2 at portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/das2 > > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 > From allenday at ucla.edu Tue Jun 7 05:46:16 2005 From: allenday at ucla.edu (Allen Day) Date: Tue, 7 Jun 2005 02:46:16 -0700 (PDT) Subject: [DAS2] /das/assay namespace Message-ID: is available for browsing on the prototype server. example queries: http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/algorithm http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/assay http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/material http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification These are more interesting: #get quantification 2753. it's a netCDF file of a HG-U133A chip #quantified/normalized with Bioconductor's GCRMA algorithm http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification/2753 #as above, but use a feature filter from genome-das to only retrieve #measurements from 10-90Mb on chrY. http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification/2753?feature.overlaps=chrY/10000000:90000000;algorithm=3 #as above, but retrieve 10-90Mb on chrY for all GCRMA-processed chips, of #which there are 661. http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification?feature.overlaps=chrY/10000000:90000000;algorithm=3 #as above, but restrict to CNS samples instead of all 661. this #filter doesn't work yet. http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification?feature.overlaps=chrY/10000000:90000000;algorithm=3;material.type=MA:central_nervous_system In principle, any feature filter can be used with the /quantification request by simply prefixing with "feature." to enable passthru to the feature filter classes on the server. In practice, none of the Affymetrix probesets are annotated with anything beyond their region and primary type of SO:PCR_product, so the only interesting filters to use deal with coordinates. It could be interesting to start attaching the Affymetrix probeset annotations from NetAffx, so you could e.g. retrieve genome-wide expression of RTKs for all CNS samples, without having to perform overlap queries to get to the annotations on the mRNA that are being assayed... I'm almost happy with my prototype -- I'll turn it into a spec document soon. -Allen From suzi at fruitfly.org Tue Jun 7 12:03:03 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Tue, 7 Jun 2005 09:03:03 -0700 Subject: [DAS2] [Bug 1803] New: indicate that two reference coordinate systems are the same In-Reply-To: <200505261857.j4QIvUYJ014139@portal.open-bio.org> References: <200505261857.j4QIvUYJ014139@portal.open-bio.org> Message-ID: <5c036e8a7297ef59d9df9dd6678e758e@fruitfly.org> A globally unique something would certainly be essential. Has this already gotten settled? On May 26, 2005, at 11:57 AM, bugzilla-daemon at portal.open-bio.org wrote: > http://bugzilla.open-bio.org/show_bug.cgi?id=1803 > > Summary: indicate that two reference coordinate systems are > the > same > Product: BioDAS > Version: 2 > Platform: All > OS/Version: All > Status: NEW > Severity: normal > Priority: P2 > Component: Spec - GET Requests > AssignedTo: das2 at portal.open-bio.org > ReportedBy: dalke at dalkescientific.com > > > If two different servers use the same coordinate system (eg, both > using the same > assembly), is there any way that a client can figure that out? > > Perhaps a server could use a globally unique name, with the agreement > that > the same name is used only if the given regions/* are identical? > > > > ------- You are receiving this mail because: ------- > You are the assignee for the bug, or are watching the assignee. > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From dalke at dalkescientific.com Thu Jun 9 15:58:38 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Thu, 9 Jun 2005 13:58:38 -0600 Subject: [DAS2] das2 spec CVS tagged Message-ID: As we just talked about, I tagged the CVS das/das2 tree with cvs tag -R -c das2-d1 The plan is that the server, client and validator work with that spec version (and its flaws), but we are free to update CVS as needed. At BOSC/ISMB we'll work on updating the spec and writing the renewal grant. Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Fri Jun 10 04:12:28 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 10 Jun 2005 02:12:28 -0600 Subject: [DAS2] latested dasypus checked in Message-ID: <968b6f54fdd5d8491f7d82e066fa92ba@dalkescientific.com> This evening I added checks for: - better reporting of where two data structures differ - tests for region/ - a simple test for sequence/ - workarounds for some gmod problems like (Should be "REGIONS" and should not have "http://http://") The architecture is holding up. There were a few places where I needed to make stronger checks but the core das2 client API hasn't changed. Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Fri Jun 10 04:30:44 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 10 Jun 2005 02:30:44 -0600 Subject: [DAS2] how to test features? Message-ID: What's the appropriate way to test features on a server where I don't know what's present? What I did with DAS/1 was search a range of a certain size and keep shifting the search range until I find something. I would like to improve on that. For example, I know all of the types in the system so I can do a type query and double-check that all the returned features have that type. There's a good chance I'll have some enormous results lists if I do that. Some queries may end up sucking up large chunks of the database. I was thinking that a "limit" option might be useful. For example, "up to 1000 features in the range 1M to 2M." 'Course then the server may need to report "returned 1000 features but 234234 matched the query." Perhaps a server may wish to enforce a max limit on the number of features even if not specified in the request? Eg, for "http://.../features/". If there is a limit, would the number be accessible by the client? Would the spec state a lower bound for what a server must support? If the number of hits is just barely over the limit, what's the right way for the client to get the remaining list of features? Andrew dalke at dalkescientific.com From allenday at ucla.edu Fri Jun 10 06:18:00 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 10 Jun 2005 03:18:00 -0700 (PDT) Subject: [DAS2] latested dasypus checked in In-Reply-To: <968b6f54fdd5d8491f7d82e066fa92ba@dalkescientific.com> References: <968b6f54fdd5d8491f7d82e066fa92ba@dalkescientific.com> Message-ID: On Fri, 10 Jun 2005, Andrew Dalke wrote: > This evening I added checks for: > > - better reporting of where two data structures differ > - tests for region/ > - a simple test for sequence/ > - workarounds for some gmod problems like > > xmlns="http://www.biodas.org/ns/das/genome/2.00" > xmlns:xlink="http://www.w3.org/1999/xlink" > > xml:base="http://http://radius.genomics.ctrl.ucla.edu/das/genome/chado/ > chado-Hsa-17/region/"> > > > (Should be "REGIONS" and should not have "http://http://") just fixed this one on the live server. > > The architecture is holding up. There were a few places > where I needed to make stronger checks but the core das2 > client API hasn't changed. > > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 > From ALoraine at ms.soph.uab.edu Fri Jun 10 10:23:27 2005 From: ALoraine at ms.soph.uab.edu (Ann Loraine) Date: Fri, 10 Jun 2005 09:23:27 -0500 Subject: [DAS2] how to test features? Message-ID: <4E4693F3D36946479044A8997EB05BD201EFE91E@phealth4.sophad.local> If you go with a limit option, you might also consider a sorting option as well. This would be useful to select high-scoring blast hits, for instance. Limits and sorting would also be useful for an analysis DAS spec. -Ann -----Original Message----- From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open-bio.org] On Behalf Of Andrew Dalke Sent: Friday, June 10, 2005 3:31 AM To: DAS/2 Subject: [DAS2] how to test features? What's the appropriate way to test features on a server where I don't know what's present? What I did with DAS/1 was search a range of a certain size and keep shifting the search range until I find something. I would like to improve on that. For example, I know all of the types in the system so I can do a type query and double-check that all the returned features have that type. There's a good chance I'll have some enormous results lists if I do that. Some queries may end up sucking up large chunks of the database. I was thinking that a "limit" option might be useful. For example, "up to 1000 features in the range 1M to 2M." 'Course then the server may need to report "returned 1000 features but 234234 matched the query." Perhaps a server may wish to enforce a max limit on the number of features even if not specified in the request? Eg, for "http://.../features/". If there is a limit, would the number be accessible by the client? Would the spec state a lower bound for what a server must support? If the number of hits is just barely over the limit, what's the right way for the client to get the remaining list of features? Andrew dalke at dalkescientific.com _______________________________________________ DAS2 mailing list DAS2 at portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/das2 From Gregg_Helt at affymetrix.com Fri Jun 10 12:41:11 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Fri, 10 Jun 2005 09:41:11 -0700 Subject: [DAS2] how to test features? Message-ID: In DAS/1 the types response can optionally include a count of the number of features available for that particular type and source. I do think this would be a useful feature to preserve in DAS/2. From that information a client/validator could potentially tune its requested range to return on average a desired number of features. I don't think a server should return only some of the features that meet the search criteria -- should return either all or none. If a server decides that a client is requesting too much data, I think servers should be able to return some sort of "returned feature count too large" error code response. And maybe in the source or versioned source response xml have an optional indication of how many features a server is willing to serve up in a single request, so clients can know this limit in advance. gregg > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Andrew Dalke > Sent: Friday, June 10, 2005 1:31 AM > To: DAS/2 > Subject: [DAS2] how to test features? > > What's the appropriate way to test features on a > server where I don't know what's present? > > What I did with DAS/1 was search a range of a > certain size and keep shifting the search range > until I find something. > > I would like to improve on that. For example, I know > all of the types in the system so I can do a type > query and double-check that all the returned features > have that type. > > There's a good chance I'll have some enormous > results lists if I do that. Some queries may end > up sucking up large chunks of the database. > > I was thinking that a "limit" option might be useful. > For example, "up to 1000 features in the range 1M to > 2M." 'Course then the server may need to report > "returned 1000 features but 234234 matched the query." > > Perhaps a server may wish to enforce a max limit > on the number of features even if not specified in > the request? Eg, for "http://.../features/". > > If there is a limit, would the number be accessible > by the client? Would the spec state a lower bound > for what a server must support? If the number of > hits is just barely over the limit, what's the right > way for the client to get the remaining list of features? > > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From dalke at dalkescientific.com Fri Jun 10 13:13:36 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 10 Jun 2005 11:13:36 -0600 Subject: [DAS2] how to test features? In-Reply-To: References: Message-ID: <171bc94b2a23d784ad5d3dc0acf34d53@dalkescientific.com> Gregg: > In DAS/1 the types response can optionally include a count of the > number > of features available for that particular type and source. I do think > this would be a useful feature to preserve in DAS/2. I don't think it would work that well. Given the way we've structured things it's possible the type/ hierarchy is shared by several feature/ hierarchies. My two mental models are: - a single server where different source/versions shares the same types/ - a server which uses someone else's types/ and regions/ as the reference, adding only features/ > From that > information a client/validator could potentially tune its requested > range to return on average a desired number of features. My shot-in-the-dark guess is that the non-uniform distribution of features lessens its usefulness. > I don't think a server should return only some of the features that > meet > the search criteria -- should return either all or none. If a server > decides that a client is requesting too much data, I think servers > should be able to return some sort of "returned feature count too > large" > error code response. I can go along with that, though I would like to know what a client is supposed to do if it gets that response and if we should specify that a server should be able to return at least (say) 10,000 features at a time. > And maybe in the source or versioned source > response xml have an optional indication of how many features a server > is willing to serve up in a single request, so clients can know this > limit in advance. In thinking some more about that - what would a client do with that information? Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Fri Jun 10 13:52:36 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 10 Jun 2005 11:52:36 -0600 Subject: [DAS2] how to test features? In-Reply-To: References: Message-ID: Ann: > If you go with a limit option, you might also consider including an > sorting option, as well. > > This would be useful to screen out low-scoring blast hits, for > instance. That makes the interface a lot more complicated because the sort order can be different than the request. Eg, "all X sorted by Y". Even worse, it could be "sorted by Y (collated as strings) and break ties by reverse order of Z (collated as numbers)." A thick client could still implement the sort of course, though at the cost of higher overhead. One proposal I made years ago was a two-part request, the first to get a list of feature identifiers, the second to get the information about a feature. That is, /feature?whatever returns The client would then figure out "Oh, I already have A2 and B so I only need to fetch A1 and A3." Then turn around do a bunch of GET requests for the missing fields. One problem with it is that to get high performance requires using HTTP/1.1 pipelining. (Another possibility is a special API to fetch a bunch of features given its URL id, but something feels wrong about it; don't know why though.) I mention it now because the feature hitlist would be relatively small even if all features are returned; there's about 10 extra bytes per name and it compresses well. But that need for pipelining is a big limitation. I don't know if it can be done even in the Python libraries I'm used to. I think it can, I'm just not sure. I don't have the experience, and there's the extra requirement for perl and java client/server support. It wouldn't help the sort problem though, except by downloading everything into the client. Andrew dalke at dalkescientific.com From Gregg_Helt at affymetrix.com Fri Jun 10 15:27:06 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Fri, 10 Jun 2005 12:27:06 -0700 Subject: [DAS2] how to test features? Message-ID: > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Andrew Dalke > Sent: Friday, June 10, 2005 10:14 AM > To: DAS/2 > Subject: Re: [DAS2] how to test features? > > Gregg: > > In DAS/1 the types response can optionally include a count of the > > number > > of features available for that particular type and source. I do think > > this would be a useful feature to preserve in DAS/2. > > I don't think it would work that well. Given the way we've > structured things it's possible the type/ hierarchy is shared > by several feature/ hierarchies. > > My two mental models are: > - a single server where different source/versions > shares the same types/ > - a server which uses someone else's types/ and regions/ > as the reference, adding only features/ I don't really see the problem with adding optional feature counts to the types response. I don't think that any established repository of genome annotations will be pointing to an external source for types, as you suggest above. That approach would affect not just feature counts but lots of other stuff in the types response, such as PROP elements and the soon-to-be added FORMAT elements. And without a _lot_ more information about what parameters were used when running the analysis, are you sure that your "BLAST" type is the same as some other site's "BLAST" type? Unless of course you copied the data from the other site in the first place, in which case we're talking about mirroring which to me is a different subject. To me the only potential problem is that without shared type ids we don't have a useful way of determining that two types from different servers (and possibly different genomes on the same server) are equivalent. But I'm far more comfortable with that situation than with the alternative, assuming that shared type ids really indicate the exact same analysis/annotation process. And we do have ways of determining that two types have some similarity -- that's what the ontology attribute is for. Furthermore, even if a DAS/2 server did refer to an external URI for a type id, it's not clear to me why that precludes it from adding a feature count attribute to the TYPE element that it returns from the types query. And the same applies to a server sharing the same types between sources and versions. Maybe this is semantics, but it seems to me that the types response is not meant to say "these are the types", but rather "these are the types and how they are used in the context of this versioned source". > > > From that > > information a client/validator could potentially tune its requested > > range to return on average a desired number of features. > > My shot-in-the-dark guess is that the non-uniform distribution > of features lessens its usefulness. Good point. > > I don't think a server should return only some of the features that > > meet > > the search criteria -- should return either all or none. If a server > > decides that a client is requesting too much data, I think servers > > should be able to return some sort of "returned feature count too > > large" > > error code response. > > I can go along with that, though I would like to know what > a client is supposed to do if it gets that response and > if we should specify that a server should be able to return at > least (say) 10,000 features at a time. > > > And maybe in the source or versioned source > > response xml have an optional indication of how many features a server > > is willing to serve up in a single request, so clients can know this > > limit in advance. > > In thinking some more about that - what would a client do > with that information? Well, since we've got alternative feature request formats, I've thought about a format that just returns a count of the features passing the filters. Which (assuming the server can respond to such a request quickly) would allow the client to "hunt around" till it found an appropriate range for the number of features the server maxes out at, or the number of features the client wants to restrict to. Another possibility if the client knows the upper limit of the server is a variant on what you suggested: > I was thinking that a "limit" option might be useful. > For example, "up to 1000 features in the range 1M to > 2M." 'Course then the server may need to report > "returned 1000 features but 234234 matched the query." But instead of limiting number of features returned within a range, have this be based on a single point, so it would be "get the 1000 features closest to this point". Not sure if this could be done as a "closest" filter (that just has a feature count) in combination with a region filter or if would need to have a combined filter that includes both a region and the count. If the latter then "get 1000 features nearest 500K on chr2" could just be something like: closest=chr2/500000:500000,1000 I know there was talk at one point about having a "get nearest neighbor" request in DAS/2. A "closest" filter would also address that functionality -- given that a feature location is seqA/pointB:pointC, then the filter for "get nearest neighbor of typeD" is: closest=seqA/pointB:pointC,1; type=typeD Would need to work out issues of what happens when there are multiple features with same location and "closest" filter only allows some of them through, or when there are multiple features that actually overlap the given point. gregg > > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From suzi at fruitfly.org Fri Jun 10 16:05:49 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Fri, 10 Jun 2005 13:05:49 -0700 Subject: [DAS2] specific aims Message-ID: As per our discussion yesterday, here they are. I'll be sending out the full outline anon (just have to adjust it to match the changes we made to the specific aims about). I'll try and tag names to sections that need to be written, but feel free to speak up if I've missed or gotten something wrong. -S -------------- next part -------------- A non-text attachment was scrubbed... Name: DAS2_specific_aims.doc Type: application/msword Size: 26624 bytes Desc: not available URL: From Gregg_Helt at affymetrix.com Fri Jun 10 16:27:08 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Fri, 10 Jun 2005 13:27:08 -0700 Subject: [DAS2] specific aims Message-ID: Adding a bit more info to what Suzi posted: We are applying for a continuation/renewal grant based on the current DAS/2 grant. The current grant expires in June 2006. This continuation would hopefully be for three years, starting in July 2006 and hopefully extending to July 2009. What Suzi posted is the start of a Specific Aims section for the grant. If you have any suggestions for what should be included (or excluded) in this grant, please post soon! The grant is due at NIH July 1, which means we really need the text finished by June 28th. Thanks, Gregg > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Suzanna Lewis > Sent: Friday, June 10, 2005 1:06 PM > To: das at biodas.org; > Cc: Mark Gibson; Nomi Harris; Sima Misra > Subject: [DAS2] specific aims > > As per our discussion yesterday, here they are. > > I'll be sending out the full outline anon (just have to > adjust it to match the changes we made to the > specific aims about). > > I'll try and tag names to sections that need to be > written, but feel free to speak up if I've missed or > gotten something wrong. > > -S > From allenday at ucla.edu Fri Jun 10 19:28:52 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 10 Jun 2005 16:28:52 -0700 (PDT) Subject: [DAS2] how to test features? In-Reply-To: References: Message-ID: Hi Gregg, I optimized the sql query, the transcript should now also take ~15s. -Allen On Fri, 10 Jun 2005, Helt,Gregg wrote: > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlap > s=chr21/22400000:22500000;type=SO:SNP > > and > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlap > s=chr21/22100000:22500000;type=SO:transcript > > Just tried them both again. The SNP request seemed to be noticeably > faster (returned in about 15 seconds) than the last time I tried it. > The transcript request seemed to still take a very long time (returned > in about 4 minutes). > > thanks, > gregg > > > > -----Original Message----- > > From: Allen Day [mailto:allenday at ucla.edu] > > Sent: Friday, June 10, 2005 12:31 PM > > To: Helt,Gregg > > Subject: RE: [DAS2] how to test features? > > > > Hi Gregg, > > > > Please send me your slow query URLs, I will use them as optimization > test > > cases. > > > > -Allen > From Gregg_Helt at affymetrix.com Thu Jun 16 11:35:27 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 16 Jun 2005 08:35:27 -0700 Subject: [DAS2] DAS/2 meeting pushed back to noon Pacific time Message-ID: By popular demand I'm shifting the regular weekly DAS/2 grant meeting today to noon Pacific time, to get around people's prior commitments. Unless anyone strongly objects, we'll make noon the set time from now on. Conference # 800-531-3250 (or 303-928-2693 if you're outside the US) Conference ID: 2879055 thanks, gregg From Gregg_Helt at affymetrix.com Thu Jun 16 13:06:52 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 16 Jun 2005 10:06:52 -0700 Subject: [DAS2] having problems with feature xml from test server Message-ID: I'm still having some problems on the client side with parsing DAS/2 feature xml from the biopackages server. Here's my test query: http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlap s=chr21/22100000:22500000;type=SO:mRNA The main problem I'm having is really due to ambiguity in the spec. In the feature xml response, the child features of an mRNA feature don't have a "parent" attribute giving the id of the parent feature. The mRNA feature does have sub-elements giving ids of its child features. But unless we specify that if there is a child/parent relationship both element in the parent and "parent" attribute in the child are required, there's no way of knowing until you've reached the end of the document whether a particular feature is a "root" feature, or whether it has a parent. And therefore you can't really implement a useful streaming parser. This came up before at the weekly meeting, but it hasn't been added to the spec change database yet - I'll add later today. thanks, gregg From Gregg_Helt at affymetrix.com Thu Jun 16 14:49:08 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 16 Jun 2005 11:49:08 -0700 Subject: [DAS2] Today's meeting agenda Message-ID: DAS/2 continuation grant Agenda for upcoming meetings at BOSC Spec Issues? Server implementation Client implementation Validation suite From Steve_Chervitz at affymetrix.com Thu Jun 16 16:44:24 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Thu, 16 Jun 2005 13:44:24 -0700 Subject: [DAS2] Re: DAS/2 meeting pushed back to noon Pacific time In-Reply-To: Message-ID: Ann's message was bounced by the DAS/2 list, not sure why, since she's on the list. Including it below. Steve --------------------------------------------------------------------------- From: Ann Loraine Date: Thu, 16 Jun 2005 13:25:20 -0500 To: "'Helt,Gregg '" , "'das2-bounces at portal.open-bio.org '" , 'DAS/2 ' Subject: RE: [DAS2] DAS/2 meeting pushed back to noon Pacific time Hi, I won't be attending due to a conflict with Arabidopsis meeting activities. See you at ISMB! btw, PlantGDB is planning to set up an Arabidopsis DAS by the end of the month. -Ann From boconnor at ucla.edu Mon Jun 20 14:04:48 2005 From: boconnor at ucla.edu (Brian O'Connor) Date: Mon, 20 Jun 2005 11:04:48 -0700 Subject: [DAS2] types and ontologies Message-ID: <42B70540.9070507@ucla.edu> Hi, I have a question about the status of this bug: http://bugzilla.open-bio.org/show_bug.cgi?id=1792. I'm working with Allen on an internal application that uses the /das/assay namespace to retrieve microarray data. What is the consensus on this bug? Are non-sequence features annotated with terms from other ontologies allowed? I know this is outside the scope of the current spec but I was curious what people think about this. Ideally I want to be able to query for which ontologies are available as well. For example something like: http://.../das/assay/chado/chado-Hsa-17/ontology/ would return an XML document describing the ontologies loaded. This could be used to filter a types query ie /das/assay/chado/chado-Hsa-17/type?namespace=foo.bar. Although I see Lincoln mentioned using a "brief" form on the type request to do essentially the same thing (bug http://bugzilla.open-bio.org/show_bug.cgi?id=1791). This seems like a reasonable way to go, how do other people feel? --Brian From Gregg_Helt at affymetrix.com Wed Jun 22 15:04:06 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Wed, 22 Jun 2005 12:04:06 -0700 Subject: [DAS2] Tentative DAS/2 meeting schedule Message-ID: Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me know what you think. gregg Thursday, June 23 1:30 PM - 3 PM Retrieval Spec 3:30 PM - 5 PM Registry and Discovery 5 PM - 6 PM Writeback Spec 6 PM - 7 PM Continuation Grant 7:00 PM Dinner Friday, June 24 1:30 PM - 4:30 PM Anything we didn't cover in first day? 5 PM -- ?? DAS/2 BOF From suzi at fruitfly.org Thu Jun 23 07:43:14 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Thu, 23 Jun 2005 07:43:14 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: References: Message-ID: <1c6f5047e8ebd3ff0ea08481b3ff1205@fruitfly.org> Where? On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me know > what > you think. > > gregg > > Thursday, June 23 > 1:30 PM - 3 PM Retrieval Spec > 3:30 PM - 5 PM Registry and Discovery > 5 PM - 6 PM Writeback Spec > 6 PM - 7 PM Continuation Grant > 7:00 PM Dinner > > Friday, June 24 > 1:30 PM - 4:30 PM Anything we didn't cover in first day? > 5 PM -- ?? DAS/2 BOF > > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From Gregg_Helt at affymetrix.com Thu Jun 23 11:19:19 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 23 Jun 2005 08:19:19 -0700 Subject: [DAS2] Tentative DAS/2 meeting schedule Message-ID: Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd floor) and figure it out from there. gregg > -----Original Message----- > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > Sent: Thursday, June 23, 2005 7:43 AM > To: Helt,Gregg > Cc: DAS/2 > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > Where? > > On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > > > Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me know > > what > > you think. > > > > gregg > > > > Thursday, June 23 > > 1:30 PM - 3 PM Retrieval Spec > > 3:30 PM - 5 PM Registry and Discovery > > 5 PM - 6 PM Writeback Spec > > 6 PM - 7 PM Continuation Grant > > 7:00 PM Dinner > > > > Friday, June 24 > > 1:30 PM - 4:30 PM Anything we didn't cover in first day? > > 5 PM -- ?? DAS/2 BOF > > > > > > _______________________________________________ > > DAS2 mailing list > > DAS2 at portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/das2 From suzi at fruitfly.org Thu Jun 23 11:29:58 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Thu, 23 Jun 2005 11:29:58 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: References: Message-ID: I may be a tad late since I have a conference call at noon. If I'm not there would someone give me a ring to let me know where to find you. (room 5219 or 510-909-7153) -S On Jun 23, 2005, at 11:19 AM, Helt,Gregg wrote: > Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd > floor) > and figure it out from there. > > gregg > >> -----Original Message----- >> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >> Sent: Thursday, June 23, 2005 7:43 AM >> To: Helt,Gregg >> Cc: DAS/2 >> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >> >> Where? >> >> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: >> >>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me know >>> what >>> you think. >>> >>> gregg >>> >>> Thursday, June 23 >>> 1:30 PM - 3 PM Retrieval Spec >>> 3:30 PM - 5 PM Registry and Discovery >>> 5 PM - 6 PM Writeback Spec >>> 6 PM - 7 PM Continuation Grant >>> 7:00 PM Dinner >>> >>> Friday, June 24 >>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? >>> 5 PM -- ?? DAS/2 BOF >>> >>> >>> _______________________________________________ >>> DAS2 mailing list >>> DAS2 at portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/das2 > From Gregg_Helt at affymetrix.com Thu Jun 23 11:30:10 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 23 Jun 2005 08:30:10 -0700 Subject: [DAS2] Notes from DAS/2 registry meeting, September 2004 Message-ID: I dug up my notes from the meeting about DAS/2 registry and discovery we had in Hinxton last September, should be attached as a doc file. A little spotty, but may be helpful for registry and discovery discussions later today. gregg -------------- next part -------------- A non-text attachment was scrubbed... Name: Das2RegistryNotes_Sep2004.doc Type: application/msword Size: 31744 bytes Desc: Das2RegistryNotes_Sep2004.doc URL: From Gregg_Helt at affymetrix.com Thu Jun 23 11:59:24 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 23 Jun 2005 08:59:24 -0700 Subject: [DAS2] More ideas for DAS/2 registry and discovery Message-ID: Here's another idea for a DAS/2 registry/discovery service that I've been thinking about for a while... -------------- next part -------------- A non-text attachment was scrubbed... Name: AnotherDas2RegistryIdea.doc Type: application/msword Size: 41984 bytes Desc: AnotherDas2RegistryIdea.doc URL: From Gregg_Helt at affymetrix.com Thu Jun 23 12:05:21 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 23 Jun 2005 09:05:21 -0700 Subject: [DAS2] Tentative DAS/2 meeting schedule Message-ID: Still trying to figure out DAS/2 meeting location today, hoping to start around 1:30 PM. Assuming we have access to a phone, for those of you who need to call in, here's the conference line info: Dial-in, domestic: 800-531-3250 International: 303-928-2693 Conference ID: 2879055 thanks, gregg > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Helt,Gregg > Sent: Thursday, June 23, 2005 11:19 AM > To: Suzanna Lewis > Cc: DAS/2 > Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > > Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd floor) > and figure it out from there. > > gregg > > > -----Original Message----- > > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > Sent: Thursday, June 23, 2005 7:43 AM > > To: Helt,Gregg > > Cc: DAS/2 > > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > > > Where? > > > > On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > > > > > Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me know > > > what > > > you think. > > > > > > gregg > > > > > > Thursday, June 23 > > > 1:30 PM - 3 PM Retrieval Spec > > > 3:30 PM - 5 PM Registry and Discovery > > > 5 PM - 6 PM Writeback Spec > > > 6 PM - 7 PM Continuation Grant > > > 7:00 PM Dinner > > > > > > Friday, June 24 > > > 1:30 PM - 4:30 PM Anything we didn't cover in first day? > > > 5 PM -- ?? DAS/2 BOF > > > > > > > > > _______________________________________________ > > > DAS2 mailing list > > > DAS2 at portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/das2 > > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From th at sanger.ac.uk Thu Jun 23 12:18:48 2005 From: th at sanger.ac.uk (Tim Hubbard) Date: Thu, 23 Jun 2005 17:18:48 +0100 Subject: [DAS2] Notes from DAS/2 registry meeting, September 2004 In-Reply-To: References: Message-ID: Hi Gregg, Hope you're all having fun out there. At 8:30 am -0700 23/6/05, Helt,Gregg wrote: >I dug up my notes from the meeting about DAS/2 registry and discovery we >had in Hinxton last September, should be attached as a doc file. A >little spotty, but may be helpful for registry and discovery discussions >later today. You might also want to take a look at the registry we've setup for DAS1 sources (=Andreas Prlic). http://das.sanger.ac.uk/registry/listServices.jsp So far the DAS sources that have been registered are mainly for proteins, however we are starting to register genomic sources and plan to use this for handling DAS sources within Ensembl shortly. This implementation has facilities built in to validate whether DAS sources are still available at regular intervals and flag ones that cannot be contacted and allows multiple registries through child/parent relationships Tim -- ------------------------------------------------------------------------- Dr Tim Hubbard email: th at sanger.ac.uk Wellcome Trust Sanger Institute Tel (direct): +44 1223 496886 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. URL: http://www.sanger.ac.uk/Users/th ------------------------------------------------------------------------- From suzi at fruitfly.org Thu Jun 23 13:45:35 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Thu, 23 Jun 2005 13:45:35 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: References: Message-ID: <4028d8d81683f8af8f71686d29e5854e@fruitfly.org> late breaking news. we're meeting at 2 in room c on the 39th flooor. On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > Still trying to figure out DAS/2 meeting location today, hoping to > start > around 1:30 PM. Assuming we have access to a phone, for those of you > who need to call in, here's the conference line info: > > Dial-in, domestic: 800-531-3250 > International: 303-928-2693 > Conference ID: 2879055 > > thanks, > gregg > >> -----Original Message----- >> From: das2-bounces at portal.open-bio.org > [mailto:das2-bounces at portal.open- >> bio.org] On Behalf Of Helt,Gregg >> Sent: Thursday, June 23, 2005 11:19 AM >> To: Suzanna Lewis >> Cc: DAS/2 >> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule >> >> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd > floor) >> and figure it out from there. >> >> gregg >> >>> -----Original Message----- >>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >>> Sent: Thursday, June 23, 2005 7:43 AM >>> To: Helt,Gregg >>> Cc: DAS/2 >>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>> >>> Where? >>> >>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: >>> >>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me > know >>>> what >>>> you think. >>>> >>>> gregg >>>> >>>> Thursday, June 23 >>>> 1:30 PM - 3 PM Retrieval Spec >>>> 3:30 PM - 5 PM Registry and Discovery >>>> 5 PM - 6 PM Writeback Spec >>>> 6 PM - 7 PM Continuation Grant >>>> 7:00 PM Dinner >>>> >>>> Friday, June 24 >>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? >>>> 5 PM -- ?? DAS/2 BOF >>>> >>>> >>>> _______________________________________________ >>>> DAS2 mailing list >>>> DAS2 at portal.open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/das2 >> >> >> _______________________________________________ >> DAS2 mailing list >> DAS2 at portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/das2 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From lstein at cshl.edu Fri Jun 24 11:14:23 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Fri, 24 Jun 2005 11:14:23 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: <4028d8d81683f8af8f71686d29e5854e@fruitfly.org> References: <4028d8d81683f8af8f71686d29e5854e@fruitfly.org> Message-ID: <200506241114.23974.lstein@cshl.edu> Hi, Are we still on for a DAS meeting (me by telephone) at 7 pm this evening? Lincoln On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: > late breaking news. > > we're meeting at 2 in room c on the 39th flooor. > > On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > > Still trying to figure out DAS/2 meeting location today, hoping to > > start > > around 1:30 PM. Assuming we have access to a phone, for those of you > > who need to call in, here's the conference line info: > > > > Dial-in, domestic: 800-531-3250 > > International: 303-928-2693 > > Conference ID: 2879055 > > > > thanks, > > gregg > > > >> -----Original Message----- > >> From: das2-bounces at portal.open-bio.org > > > > [mailto:das2-bounces at portal.open- > > > >> bio.org] On Behalf Of Helt,Gregg > >> Sent: Thursday, June 23, 2005 11:19 AM > >> To: Suzanna Lewis > >> Cc: DAS/2 > >> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > >> > >> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd > > > > floor) > > > >> and figure it out from there. > >> > >> gregg > >> > >>> -----Original Message----- > >>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] > >>> Sent: Thursday, June 23, 2005 7:43 AM > >>> To: Helt,Gregg > >>> Cc: DAS/2 > >>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > >>> > >>> Where? > >>> > >>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > >>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me > > > > know > > > >>>> what > >>>> you think. > >>>> > >>>> gregg > >>>> > >>>> Thursday, June 23 > >>>> 1:30 PM - 3 PM Retrieval Spec > >>>> 3:30 PM - 5 PM Registry and Discovery > >>>> 5 PM - 6 PM Writeback Spec > >>>> 6 PM - 7 PM Continuation Grant > >>>> 7:00 PM Dinner > >>>> > >>>> Friday, June 24 > >>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? > >>>> 5 PM -- ?? DAS/2 BOF > >>>> > >>>> > >>>> _______________________________________________ > >>>> DAS2 mailing list > >>>> DAS2 at portal.open-bio.org > >>>> http://portal.open-bio.org/mailman/listinfo/das2 > >> > >> _______________________________________________ > >> DAS2 mailing list > >> DAS2 at portal.open-bio.org > >> http://portal.open-bio.org/mailman/listinfo/das2 > > > > _______________________________________________ > > DAS2 mailing list > > DAS2 at portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/das2 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 -- Lincoln Stein lstein at cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From Gregg_Helt at affymetrix.com Fri Jun 24 16:45:04 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Fri, 24 Jun 2005 13:45:04 -0700 Subject: [DAS2] Tentative DAS/2 meeting schedule Message-ID: Yep, will that work for you? We're holding it in the Ambassador II room (where BOSC is), the hotel folks are supposed to install a speakerphone for us. Same teleconference numbers: Phone: 800-531-3250 Id: 2879055 thanks, gregg > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Lincoln Stein > Sent: Friday, June 24, 2005 11:14 AM > To: das2 at portal.open-bio.org > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > Hi, > > Are we still on for a DAS meeting (me by telephone) at 7 pm this evening? > > Lincoln > > On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: > > late breaking news. > > > > we're meeting at 2 in room c on the 39th flooor. > > > > On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > > > Still trying to figure out DAS/2 meeting location today, hoping to > > > start > > > around 1:30 PM. Assuming we have access to a phone, for those of you > > > who need to call in, here's the conference line info: > > > > > > Dial-in, domestic: 800-531-3250 > > > International: 303-928-2693 > > > Conference ID: 2879055 > > > > > > thanks, > > > gregg > > > > > >> -----Original Message----- > > >> From: das2-bounces at portal.open-bio.org > > > > > > [mailto:das2-bounces at portal.open- > > > > > >> bio.org] On Behalf Of Helt,Gregg > > >> Sent: Thursday, June 23, 2005 11:19 AM > > >> To: Suzanna Lewis > > >> Cc: DAS/2 > > >> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > > >> > > >> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd > > > > > > floor) > > > > > >> and figure it out from there. > > >> > > >> gregg > > >> > > >>> -----Original Message----- > > >>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > >>> Sent: Thursday, June 23, 2005 7:43 AM > > >>> To: Helt,Gregg > > >>> Cc: DAS/2 > > >>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >>> > > >>> Where? > > >>> > > >>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > > >>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me > > > > > > know > > > > > >>>> what > > >>>> you think. > > >>>> > > >>>> gregg > > >>>> > > >>>> Thursday, June 23 > > >>>> 1:30 PM - 3 PM Retrieval Spec > > >>>> 3:30 PM - 5 PM Registry and Discovery > > >>>> 5 PM - 6 PM Writeback Spec > > >>>> 6 PM - 7 PM Continuation Grant > > >>>> 7:00 PM Dinner > > >>>> > > >>>> Friday, June 24 > > >>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? > > >>>> 5 PM -- ?? DAS/2 BOF > > >>>> > > >>>> > > >>>> _______________________________________________ > > >>>> DAS2 mailing list > > >>>> DAS2 at portal.open-bio.org > > >>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >> > > >> _______________________________________________ > > >> DAS2 mailing list > > >> DAS2 at portal.open-bio.org > > >> http://portal.open-bio.org/mailman/listinfo/das2 > > > > > > _______________________________________________ > > > DAS2 mailing list > > > DAS2 at portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/das2 > > > > _______________________________________________ > > DAS2 mailing list > > DAS2 at portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/das2 > > -- > Lincoln Stein > lstein at cshl.edu > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From suzi at fruitfly.org Fri Jun 24 17:26:50 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Fri, 24 Jun 2005 17:26:50 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: References: Message-ID: <13255739cf06fa840d4145fc878b3410@fruitfly.org> I may be late, but I'll be there (Is anyone is bringing food?) On Jun 24, 2005, at 4:45 PM, Helt,Gregg wrote: > Yep, will that work for you? We're holding it in the Ambassador II > room > (where BOSC is), the hotel folks are supposed to install a speakerphone > for us. Same teleconference numbers: > Phone: 800-531-3250 > Id: 2879055 > > thanks, > gregg > >> -----Original Message----- >> From: das2-bounces at portal.open-bio.org > [mailto:das2-bounces at portal.open- >> bio.org] On Behalf Of Lincoln Stein >> Sent: Friday, June 24, 2005 11:14 AM >> To: das2 at portal.open-bio.org >> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >> >> Hi, >> >> Are we still on for a DAS meeting (me by telephone) at 7 pm this > evening? >> >> Lincoln >> >> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: >>> late breaking news. >>> >>> we're meeting at 2 in room c on the 39th flooor. >>> >>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: >>>> Still trying to figure out DAS/2 meeting location today, hoping to >>>> start >>>> around 1:30 PM. Assuming we have access to a phone, for those of > you >>>> who need to call in, here's the conference line info: >>>> >>>> Dial-in, domestic: 800-531-3250 >>>> International: 303-928-2693 >>>> Conference ID: 2879055 >>>> >>>> thanks, >>>> gregg >>>> >>>>> -----Original Message----- >>>>> From: das2-bounces at portal.open-bio.org >>>> >>>> [mailto:das2-bounces at portal.open- >>>> >>>>> bio.org] On Behalf Of Helt,Gregg >>>>> Sent: Thursday, June 23, 2005 11:19 AM >>>>> To: Suzanna Lewis >>>>> Cc: DAS/2 >>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule >>>>> >>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd >>>> >>>> floor) >>>> >>>>> and figure it out from there. >>>>> >>>>> gregg >>>>> >>>>>> -----Original Message----- >>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >>>>>> Sent: Thursday, June 23, 2005 7:43 AM >>>>>> To: Helt,Gregg >>>>>> Cc: DAS/2 >>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>> >>>>>> Where? >>>>>> >>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: >>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me >>>> >>>> know >>>> >>>>>>> what >>>>>>> you think. >>>>>>> >>>>>>> gregg >>>>>>> >>>>>>> Thursday, June 23 >>>>>>> 1:30 PM - 3 PM Retrieval Spec >>>>>>> 3:30 PM - 5 PM Registry and Discovery >>>>>>> 5 PM - 6 PM Writeback Spec >>>>>>> 6 PM - 7 PM Continuation Grant >>>>>>> 7:00 PM Dinner >>>>>>> >>>>>>> Friday, June 24 >>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? >>>>>>> 5 PM -- ?? DAS/2 BOF >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> DAS2 mailing list >>>>>>> DAS2 at portal.open-bio.org >>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>> >>>>> _______________________________________________ >>>>> DAS2 mailing list >>>>> DAS2 at portal.open-bio.org >>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>> >>>> _______________________________________________ >>>> DAS2 mailing list >>>> DAS2 at portal.open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/das2 >>> >>> _______________________________________________ >>> DAS2 mailing list >>> DAS2 at portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/das2 >> >> -- >> Lincoln Stein >> lstein at cshl.edu >> Cold Spring Harbor Laboratory >> 1 Bungtown Road >> Cold Spring Harbor, NY 11724 >> (516) 367-8380 (voice) >> (516) 367-8389 (fax) >> _______________________________________________ >> DAS2 mailing list >> DAS2 at portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/das2 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From lstein at cshl.edu Fri Jun 24 14:18:10 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Fri, 24 Jun 2005 14:18:10 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: References: Message-ID: <200506241418.10570.lstein@cshl.edu> Sounds good! Lincoln On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: > Yep, will that work for you? We're holding it in the Ambassador II room > (where BOSC is), the hotel folks are supposed to install a speakerphone > for us. Same teleconference numbers: > Phone: 800-531-3250 > Id: 2879055 > > thanks, > gregg > > > -----Original Message----- > > From: das2-bounces at portal.open-bio.org > > [mailto:das2-bounces at portal.open- > > > bio.org] On Behalf Of Lincoln Stein > > Sent: Friday, June 24, 2005 11:14 AM > > To: das2 at portal.open-bio.org > > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > > > Hi, > > > > Are we still on for a DAS meeting (me by telephone) at 7 pm this > > evening? > > > Lincoln > > > > On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: > > > late breaking news. > > > > > > we're meeting at 2 in room c on the 39th flooor. > > > > > > On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > > > > Still trying to figure out DAS/2 meeting location today, hoping to > > > > start > > > > around 1:30 PM. Assuming we have access to a phone, for those of > > you > > > > > who need to call in, here's the conference line info: > > > > > > > > Dial-in, domestic: 800-531-3250 > > > > International: 303-928-2693 > > > > Conference ID: 2879055 > > > > > > > > thanks, > > > > gregg > > > > > > > >> -----Original Message----- > > > >> From: das2-bounces at portal.open-bio.org > > > > > > > > [mailto:das2-bounces at portal.open- > > > > > > > >> bio.org] On Behalf Of Helt,Gregg > > > >> Sent: Thursday, June 23, 2005 11:19 AM > > > >> To: Suzanna Lewis > > > >> Cc: DAS/2 > > > >> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > > > >> > > > >> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd > > > > > > > > floor) > > > > > > > >> and figure it out from there. > > > >> > > > >> gregg > > > >> > > > >>> -----Original Message----- > > > >>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > > >>> Sent: Thursday, June 23, 2005 7:43 AM > > > >>> To: Helt,Gregg > > > >>> Cc: DAS/2 > > > >>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > > >>> > > > >>> Where? > > > >>> > > > >>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > > > >>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me > > > > > > > > know > > > > > > > >>>> what > > > >>>> you think. > > > >>>> > > > >>>> gregg > > > >>>> > > > >>>> Thursday, June 23 > > > >>>> 1:30 PM - 3 PM Retrieval Spec > > > >>>> 3:30 PM - 5 PM Registry and Discovery > > > >>>> 5 PM - 6 PM Writeback Spec > > > >>>> 6 PM - 7 PM Continuation Grant > > > >>>> 7:00 PM Dinner > > > >>>> > > > >>>> Friday, June 24 > > > >>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? > > > >>>> 5 PM -- ?? DAS/2 BOF > > > >>>> > > > >>>> > > > >>>> _______________________________________________ > > > >>>> DAS2 mailing list > > > >>>> DAS2 at portal.open-bio.org > > > >>>> http://portal.open-bio.org/mailman/listinfo/das2 > > > >> > > > >> _______________________________________________ > > > >> DAS2 mailing list > > > >> DAS2 at portal.open-bio.org > > > >> http://portal.open-bio.org/mailman/listinfo/das2 > > > > > > > > _______________________________________________ > > > > DAS2 mailing list > > > > DAS2 at portal.open-bio.org > > > > http://portal.open-bio.org/mailman/listinfo/das2 > > > > > > _______________________________________________ > > > DAS2 mailing list > > > DAS2 at portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/das2 > > > > -- > > Lincoln Stein > > lstein at cshl.edu > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > _______________________________________________ > > DAS2 mailing list > > DAS2 at portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/das2 -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From Gregg_Helt at affymetrix.com Fri Jun 24 19:08:33 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Fri, 24 Jun 2005 16:08:33 -0700 Subject: [DAS2] Tentative DAS/2 meeting schedule Message-ID: Apologies, looks like we lost the room I was planning to meet in (and the speakerphone). I think we better reschedule. How about starting up again on Sunday? Gregg > -----Original Message----- > From: Lincoln Stein [mailto:lstein at cshl.edu] > Sent: Friday, June 24, 2005 2:18 PM > To: Helt,Gregg > Cc: das2 at portal.open-bio.org > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > Sounds good! > > Lincoln > > On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: > > Yep, will that work for you? We're holding it in the Ambassador II room > > (where BOSC is), the hotel folks are supposed to install a speakerphone > > for us. Same teleconference numbers: > > Phone: 800-531-3250 > > Id: 2879055 > > > > thanks, > > gregg > > > > > -----Original Message----- > > > From: das2-bounces at portal.open-bio.org > > > > [mailto:das2-bounces at portal.open- > > > > > bio.org] On Behalf Of Lincoln Stein > > > Sent: Friday, June 24, 2005 11:14 AM > > > To: das2 at portal.open-bio.org > > > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > > > > > Hi, > > > > > > Are we still on for a DAS meeting (me by telephone) at 7 pm this > > > > evening? > > > > > Lincoln > > > > > > On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: > > > > late breaking news. > > > > > > > > we're meeting at 2 in room c on the 39th flooor. > > > > > > > > On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > > > > > Still trying to figure out DAS/2 meeting location today, hoping to > > > > > start > > > > > around 1:30 PM. Assuming we have access to a phone, for those of > > > > you > > > > > > > who need to call in, here's the conference line info: > > > > > > > > > > Dial-in, domestic: 800-531-3250 > > > > > International: 303-928-2693 > > > > > Conference ID: 2879055 > > > > > > > > > > thanks, > > > > > gregg > > > > > > > > > >> -----Original Message----- > > > > >> From: das2-bounces at portal.open-bio.org > > > > > > > > > > [mailto:das2-bounces at portal.open- > > > > > > > > > >> bio.org] On Behalf Of Helt,Gregg > > > > >> Sent: Thursday, June 23, 2005 11:19 AM > > > > >> To: Suzanna Lewis > > > > >> Cc: DAS/2 > > > > >> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > > > > >> > > > > >> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd > > > > > > > > > > floor) > > > > > > > > > >> and figure it out from there. > > > > >> > > > > >> gregg > > > > >> > > > > >>> -----Original Message----- > > > > >>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > > > >>> Sent: Thursday, June 23, 2005 7:43 AM > > > > >>> To: Helt,Gregg > > > > >>> Cc: DAS/2 > > > > >>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > > > >>> > > > > >>> Where? > > > > >>> > > > > >>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > > > > >>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me > > > > > > > > > > know > > > > > > > > > >>>> what > > > > >>>> you think. > > > > >>>> > > > > >>>> gregg > > > > >>>> > > > > >>>> Thursday, June 23 > > > > >>>> 1:30 PM - 3 PM Retrieval Spec > > > > >>>> 3:30 PM - 5 PM Registry and Discovery > > > > >>>> 5 PM - 6 PM Writeback Spec > > > > >>>> 6 PM - 7 PM Continuation Grant > > > > >>>> 7:00 PM Dinner > > > > >>>> > > > > >>>> Friday, June 24 > > > > >>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? > > > > >>>> 5 PM -- ?? DAS/2 BOF > > > > >>>> > > > > >>>> > > > > >>>> _______________________________________________ > > > > >>>> DAS2 mailing list > > > > >>>> DAS2 at portal.open-bio.org > > > > >>>> http://portal.open-bio.org/mailman/listinfo/das2 > > > > >> > > > > >> _______________________________________________ > > > > >> DAS2 mailing list > > > > >> DAS2 at portal.open-bio.org > > > > >> http://portal.open-bio.org/mailman/listinfo/das2 > > > > > > > > > > _______________________________________________ > > > > > DAS2 mailing list > > > > > DAS2 at portal.open-bio.org > > > > > http://portal.open-bio.org/mailman/listinfo/das2 > > > > > > > > _______________________________________________ > > > > DAS2 mailing list > > > > DAS2 at portal.open-bio.org > > > > http://portal.open-bio.org/mailman/listinfo/das2 > > > > > > -- > > > Lincoln Stein > > > lstein at cshl.edu > > > Cold Spring Harbor Laboratory > > > 1 Bungtown Road > > > Cold Spring Harbor, NY 11724 > > > (516) 367-8380 (voice) > > > (516) 367-8389 (fax) > > > _______________________________________________ > > > DAS2 mailing list > > > DAS2 at portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/das2 > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 From suzi at fruitfly.org Fri Jun 24 19:56:23 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Fri, 24 Jun 2005 19:56:23 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: References: Message-ID: <8a4e2260f0f734d92b43b789f93dc940@fruitfly.org> Ah, I was wondering why I didn't find you there. Sunday morn would work for me. On Jun 24, 2005, at 7:08 PM, Helt,Gregg wrote: > Apologies, looks like we lost the room I was planning to meet in (and > the speakerphone). I think we better reschedule. How about starting > up > again on Sunday? > > Gregg > > >> -----Original Message----- >> From: Lincoln Stein [mailto:lstein at cshl.edu] >> Sent: Friday, June 24, 2005 2:18 PM >> To: Helt,Gregg >> Cc: das2 at portal.open-bio.org >> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >> >> Sounds good! >> >> Lincoln >> >> On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: >>> Yep, will that work for you? We're holding it in the Ambassador II > room >>> (where BOSC is), the hotel folks are supposed to install a > speakerphone >>> for us. Same teleconference numbers: >>> Phone: 800-531-3250 >>> Id: 2879055 >>> >>> thanks, >>> gregg >>> >>>> -----Original Message----- >>>> From: das2-bounces at portal.open-bio.org >>> >>> [mailto:das2-bounces at portal.open- >>> >>>> bio.org] On Behalf Of Lincoln Stein >>>> Sent: Friday, June 24, 2005 11:14 AM >>>> To: das2 at portal.open-bio.org >>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>> >>>> Hi, >>>> >>>> Are we still on for a DAS meeting (me by telephone) at 7 pm this >>> >>> evening? >>> >>>> Lincoln >>>> >>>> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: >>>>> late breaking news. >>>>> >>>>> we're meeting at 2 in room c on the 39th flooor. >>>>> >>>>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: >>>>>> Still trying to figure out DAS/2 meeting location today, > hoping to >>>>>> start >>>>>> around 1:30 PM. Assuming we have access to a phone, for those > of >>> >>> you >>> >>>>>> who need to call in, here's the conference line info: >>>>>> >>>>>> Dial-in, domestic: 800-531-3250 >>>>>> International: 303-928-2693 >>>>>> Conference ID: 2879055 >>>>>> >>>>>> thanks, >>>>>> gregg >>>>>> >>>>>>> -----Original Message----- >>>>>>> From: das2-bounces at portal.open-bio.org >>>>>> >>>>>> [mailto:das2-bounces at portal.open- >>>>>> >>>>>>> bio.org] On Behalf Of Helt,Gregg >>>>>>> Sent: Thursday, June 23, 2005 11:19 AM >>>>>>> To: Suzanna Lewis >>>>>>> Cc: DAS/2 >>>>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule >>>>>>> >>>>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby > (3rd >>>>>> >>>>>> floor) >>>>>> >>>>>>> and figure it out from there. >>>>>>> >>>>>>> gregg >>>>>>> >>>>>>>> -----Original Message----- >>>>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >>>>>>>> Sent: Thursday, June 23, 2005 7:43 AM >>>>>>>> To: Helt,Gregg >>>>>>>> Cc: DAS/2 >>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>> >>>>>>>> Where? >>>>>>>> >>>>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: >>>>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let > me >>>>>> >>>>>> know >>>>>> >>>>>>>>> what >>>>>>>>> you think. >>>>>>>>> >>>>>>>>> gregg >>>>>>>>> >>>>>>>>> Thursday, June 23 >>>>>>>>> 1:30 PM - 3 PM Retrieval Spec >>>>>>>>> 3:30 PM - 5 PM Registry and Discovery >>>>>>>>> 5 PM - 6 PM Writeback Spec >>>>>>>>> 6 PM - 7 PM Continuation Grant >>>>>>>>> 7:00 PM Dinner >>>>>>>>> >>>>>>>>> Friday, June 24 >>>>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? >>>>>>>>> 5 PM -- ?? DAS/2 BOF >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> DAS2 mailing list >>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>> >>>>>>> _______________________________________________ >>>>>>> DAS2 mailing list >>>>>>> DAS2 at portal.open-bio.org >>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>> >>>>>> _______________________________________________ >>>>>> DAS2 mailing list >>>>>> DAS2 at portal.open-bio.org >>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>> >>>>> _______________________________________________ >>>>> DAS2 mailing list >>>>> DAS2 at portal.open-bio.org >>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>> >>>> -- >>>> Lincoln Stein >>>> lstein at cshl.edu >>>> Cold Spring Harbor Laboratory >>>> 1 Bungtown Road >>>> Cold Spring Harbor, NY 11724 >>>> (516) 367-8380 (voice) >>>> (516) 367-8389 (fax) >>>> _______________________________________________ >>>> DAS2 mailing list >>>> DAS2 at portal.open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/das2 >> >> -- >> Lincoln D. Stein >> Cold Spring Harbor Laboratory >> 1 Bungtown Road >> Cold Spring Harbor, NY 11724 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From suzi at fruitfly.org Sat Jun 25 21:30:51 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Sat, 25 Jun 2005 21:30:51 -0400 Subject: [DAS2] Monday for next meeting Message-ID: <56b5ba368d05b3346567807d1a1bdedd@fruitfly.org> Hi all, just received a voice message from Gregg. He can't arrange a meeting room for Sunday, but will/can do this for Monday (27th). Details to follow. This is just to let you know that Sunday is a day off (as far as DAS work). best, S From Steve_Chervitz at affymetrix.com Sun Jun 26 11:26:23 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Sun, 26 Jun 2005 08:26:23 -0700 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: <8a4e2260f0f734d92b43b789f93dc940@fruitfly.org> Message-ID: Is there a meeting on for today? Did it happen already? Gregg: Are you going to be back at ISMB today? Steve > From: Suzanna Lewis > Date: Fri, 24 Jun 2005 19:56:23 -0400 > To: "Helt,Gregg" > Cc: > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > Ah, I was wondering why I didn't find you there. Sunday morn would work > for me. > > On Jun 24, 2005, at 7:08 PM, Helt,Gregg wrote: > >> Apologies, looks like we lost the room I was planning to meet in (and >> the speakerphone). I think we better reschedule. How about starting >> up >> again on Sunday? >> >> Gregg >> >> >>> -----Original Message----- >>> From: Lincoln Stein [mailto:lstein at cshl.edu] >>> Sent: Friday, June 24, 2005 2:18 PM >>> To: Helt,Gregg >>> Cc: das2 at portal.open-bio.org >>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>> >>> Sounds good! >>> >>> Lincoln >>> >>> On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: >>>> Yep, will that work for you? We're holding it in the Ambassador II >> room >>>> (where BOSC is), the hotel folks are supposed to install a >> speakerphone >>>> for us. Same teleconference numbers: >>>> Phone: 800-531-3250 >>>> Id: 2879055 >>>> >>>> thanks, >>>> gregg >>>> >>>>> -----Original Message----- >>>>> From: das2-bounces at portal.open-bio.org >>>> >>>> [mailto:das2-bounces at portal.open- >>>> >>>>> bio.org] On Behalf Of Lincoln Stein >>>>> Sent: Friday, June 24, 2005 11:14 AM >>>>> To: das2 at portal.open-bio.org >>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>> >>>>> Hi, >>>>> >>>>> Are we still on for a DAS meeting (me by telephone) at 7 pm this >>>> >>>> evening? >>>> >>>>> Lincoln >>>>> >>>>> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: >>>>>> late breaking news. >>>>>> >>>>>> we're meeting at 2 in room c on the 39th flooor. >>>>>> >>>>>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: >>>>>>> Still trying to figure out DAS/2 meeting location today, >> hoping to >>>>>>> start >>>>>>> around 1:30 PM. Assuming we have access to a phone, for those >> of >>>> >>>> you >>>> >>>>>>> who need to call in, here's the conference line info: >>>>>>> >>>>>>> Dial-in, domestic: 800-531-3250 >>>>>>> International: 303-928-2693 >>>>>>> Conference ID: 2879055 >>>>>>> >>>>>>> thanks, >>>>>>> gregg >>>>>>> >>>>>>>> -----Original Message----- >>>>>>>> From: das2-bounces at portal.open-bio.org >>>>>>> >>>>>>> [mailto:das2-bounces at portal.open- >>>>>>> >>>>>>>> bio.org] On Behalf Of Helt,Gregg >>>>>>>> Sent: Thursday, June 23, 2005 11:19 AM >>>>>>>> To: Suzanna Lewis >>>>>>>> Cc: DAS/2 >>>>>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>> >>>>>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby >> (3rd >>>>>>> >>>>>>> floor) >>>>>>> >>>>>>>> and figure it out from there. >>>>>>>> >>>>>>>> gregg >>>>>>>> >>>>>>>>> -----Original Message----- >>>>>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >>>>>>>>> Sent: Thursday, June 23, 2005 7:43 AM >>>>>>>>> To: Helt,Gregg >>>>>>>>> Cc: DAS/2 >>>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>>> >>>>>>>>> Where? >>>>>>>>> >>>>>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: >>>>>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let >> me >>>>>>> >>>>>>> know >>>>>>> >>>>>>>>>> what >>>>>>>>>> you think. >>>>>>>>>> >>>>>>>>>> gregg >>>>>>>>>> >>>>>>>>>> Thursday, June 23 >>>>>>>>>> 1:30 PM - 3 PM Retrieval Spec >>>>>>>>>> 3:30 PM - 5 PM Registry and Discovery >>>>>>>>>> 5 PM - 6 PM Writeback Spec >>>>>>>>>> 6 PM - 7 PM Continuation Grant >>>>>>>>>> 7:00 PM Dinner >>>>>>>>>> >>>>>>>>>> Friday, June 24 >>>>>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? >>>>>>>>>> 5 PM -- ?? DAS/2 BOF >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> DAS2 mailing list >>>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> DAS2 mailing list >>>>>>>> DAS2 at portal.open-bio.org >>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>> >>>>>>> _______________________________________________ >>>>>>> DAS2 mailing list >>>>>>> DAS2 at portal.open-bio.org >>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>> >>>>>> _______________________________________________ >>>>>> DAS2 mailing list >>>>>> DAS2 at portal.open-bio.org >>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>> >>>>> -- >>>>> Lincoln Stein >>>>> lstein at cshl.edu >>>>> Cold Spring Harbor Laboratory >>>>> 1 Bungtown Road >>>>> Cold Spring Harbor, NY 11724 >>>>> (516) 367-8380 (voice) >>>>> (516) 367-8389 (fax) >>>>> _______________________________________________ >>>>> DAS2 mailing list >>>>> DAS2 at portal.open-bio.org >>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>> >>> -- >>> Lincoln D. Stein >>> Cold Spring Harbor Laboratory >>> 1 Bungtown Road >>> Cold Spring Harbor, NY 11724 >> >> _______________________________________________ >> DAS2 mailing list >> DAS2 at portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/das2 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From suzi at fruitfly.org Sun Jun 26 11:29:26 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Sun, 26 Jun 2005 11:29:26 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: References: Message-ID: <9247240106245d1ec052ca92d38d3c02@fruitfly.org> No meeting today. Gregg will be back latter today to arrange a room for tomorrow and let us know. (appears like my last mail didn't get through) On Jun 26, 2005, at 11:26 AM, Chervitz, Steve wrote: > Is there a meeting on for today? Did it happen already? Gregg: Are you > going > to be back at ISMB today? > > Steve > > >> From: Suzanna Lewis >> Date: Fri, 24 Jun 2005 19:56:23 -0400 >> To: "Helt,Gregg" >> Cc: >> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >> >> Ah, I was wondering why I didn't find you there. Sunday morn would >> work >> for me. >> >> On Jun 24, 2005, at 7:08 PM, Helt,Gregg wrote: >> >>> Apologies, looks like we lost the room I was planning to meet in (and >>> the speakerphone). I think we better reschedule. How about starting >>> up >>> again on Sunday? >>> >>> Gregg >>> >>> >>>> -----Original Message----- >>>> From: Lincoln Stein [mailto:lstein at cshl.edu] >>>> Sent: Friday, June 24, 2005 2:18 PM >>>> To: Helt,Gregg >>>> Cc: das2 at portal.open-bio.org >>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>> >>>> Sounds good! >>>> >>>> Lincoln >>>> >>>> On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: >>>>> Yep, will that work for you? We're holding it in the Ambassador II >>> room >>>>> (where BOSC is), the hotel folks are supposed to install a >>> speakerphone >>>>> for us. Same teleconference numbers: >>>>> Phone: 800-531-3250 >>>>> Id: 2879055 >>>>> >>>>> thanks, >>>>> gregg >>>>> >>>>>> -----Original Message----- >>>>>> From: das2-bounces at portal.open-bio.org >>>>> >>>>> [mailto:das2-bounces at portal.open- >>>>> >>>>>> bio.org] On Behalf Of Lincoln Stein >>>>>> Sent: Friday, June 24, 2005 11:14 AM >>>>>> To: das2 at portal.open-bio.org >>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>> >>>>>> Hi, >>>>>> >>>>>> Are we still on for a DAS meeting (me by telephone) at 7 pm this >>>>> >>>>> evening? >>>>> >>>>>> Lincoln >>>>>> >>>>>> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: >>>>>>> late breaking news. >>>>>>> >>>>>>> we're meeting at 2 in room c on the 39th flooor. >>>>>>> >>>>>>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: >>>>>>>> Still trying to figure out DAS/2 meeting location today, >>> hoping to >>>>>>>> start >>>>>>>> around 1:30 PM. Assuming we have access to a phone, for those >>> of >>>>> >>>>> you >>>>> >>>>>>>> who need to call in, here's the conference line info: >>>>>>>> >>>>>>>> Dial-in, domestic: 800-531-3250 >>>>>>>> International: 303-928-2693 >>>>>>>> Conference ID: 2879055 >>>>>>>> >>>>>>>> thanks, >>>>>>>> gregg >>>>>>>> >>>>>>>>> -----Original Message----- >>>>>>>>> From: das2-bounces at portal.open-bio.org >>>>>>>> >>>>>>>> [mailto:das2-bounces at portal.open- >>>>>>>> >>>>>>>>> bio.org] On Behalf Of Helt,Gregg >>>>>>>>> Sent: Thursday, June 23, 2005 11:19 AM >>>>>>>>> To: Suzanna Lewis >>>>>>>>> Cc: DAS/2 >>>>>>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>>> >>>>>>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby >>> (3rd >>>>>>>> >>>>>>>> floor) >>>>>>>> >>>>>>>>> and figure it out from there. >>>>>>>>> >>>>>>>>> gregg >>>>>>>>> >>>>>>>>>> -----Original Message----- >>>>>>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >>>>>>>>>> Sent: Thursday, June 23, 2005 7:43 AM >>>>>>>>>> To: Helt,Gregg >>>>>>>>>> Cc: DAS/2 >>>>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>>>> >>>>>>>>>> Where? >>>>>>>>>> >>>>>>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: >>>>>>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let >>> me >>>>>>>> >>>>>>>> know >>>>>>>> >>>>>>>>>>> what >>>>>>>>>>> you think. >>>>>>>>>>> >>>>>>>>>>> gregg >>>>>>>>>>> >>>>>>>>>>> Thursday, June 23 >>>>>>>>>>> 1:30 PM - 3 PM Retrieval Spec >>>>>>>>>>> 3:30 PM - 5 PM Registry and Discovery >>>>>>>>>>> 5 PM - 6 PM Writeback Spec >>>>>>>>>>> 6 PM - 7 PM Continuation Grant >>>>>>>>>>> 7:00 PM Dinner >>>>>>>>>>> >>>>>>>>>>> Friday, June 24 >>>>>>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? >>>>>>>>>>> 5 PM -- ?? DAS/2 BOF >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> DAS2 mailing list >>>>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> DAS2 mailing list >>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> DAS2 mailing list >>>>>>>> DAS2 at portal.open-bio.org >>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>> >>>>>>> _______________________________________________ >>>>>>> DAS2 mailing list >>>>>>> DAS2 at portal.open-bio.org >>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>> >>>>>> -- >>>>>> Lincoln Stein >>>>>> lstein at cshl.edu >>>>>> Cold Spring Harbor Laboratory >>>>>> 1 Bungtown Road >>>>>> Cold Spring Harbor, NY 11724 >>>>>> (516) 367-8380 (voice) >>>>>> (516) 367-8389 (fax) >>>>>> _______________________________________________ >>>>>> DAS2 mailing list >>>>>> DAS2 at portal.open-bio.org >>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>> >>>> -- >>>> Lincoln D. Stein >>>> Cold Spring Harbor Laboratory >>>> 1 Bungtown Road >>>> Cold Spring Harbor, NY 11724 >>> >>> _______________________________________________ >>> DAS2 mailing list >>> DAS2 at portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/das2 >> >> _______________________________________________ >> DAS2 mailing list >> DAS2 at portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/das2 > From lstein at cshl.edu Sun Jun 26 13:08:35 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Sun, 26 Jun 2005 13:08:35 -0400 Subject: [DAS2] Monday for next meeting In-Reply-To: <56b5ba368d05b3346567807d1a1bdedd@fruitfly.org> References: <56b5ba368d05b3346567807d1a1bdedd@fruitfly.org> Message-ID: <200506261308.36358.lstein@cshl.edu> Hi Suzi, I'm not shedding any tears over this! Lincoln On Saturday 25 June 2005 09:30 pm, Suzanna Lewis wrote: > Hi all, > > just received a voice message from Gregg. He can't arrange a meeting > room for Sunday, but will/can do this for Monday (27th). Details to > follow. This is just to let you know that Sunday is a day off (as far > as DAS work). > > best, S > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From Gregg_Helt at affymetrix.com Sun Jun 26 18:35:19 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Sun, 26 Jun 2005 15:35:19 -0700 Subject: [DAS2] DAS/2 meeting schedule for Monday Message-ID: I've reserved a room for a DAS/2 meeting tomorrow (Monday), Duluth (on the 5th floor), from 2PM to 6PM Eastern time. It also comes with a better speakerphone than what we had last time. Lincoln and Allen, please let me know as soon as possible if you can't make it! With a four hour window, I'm hoping you can both teleconference in for at least part of the meeting. I've also tentatively reserved the same room for 2PM to 5 PM Tuesday, Eastern time. Conference phone #: 800-531-3250 Conference id: 2879055 gregg > -----Original Message----- > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > Sent: Sunday, June 26, 2005 11:29 AM > To: Chervitz, Steve > Cc: Helt,Gregg; das2 at portal.open-bio.org > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > No meeting today. Gregg will be back latter today to arrange a room for > tomorrow and let us know. (appears like my last mail didn't get > through) > > > On Jun 26, 2005, at 11:26 AM, Chervitz, Steve wrote: > > > Is there a meeting on for today? Did it happen already? Gregg: Are you > > going > > to be back at ISMB today? > > > > Steve > > > > > >> From: Suzanna Lewis > >> Date: Fri, 24 Jun 2005 19:56:23 -0400 > >> To: "Helt,Gregg" > >> Cc: > >> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > >> > >> Ah, I was wondering why I didn't find you there. Sunday morn would > >> work > >> for me. > >> > >> On Jun 24, 2005, at 7:08 PM, Helt,Gregg wrote: > >> > >>> Apologies, looks like we lost the room I was planning to meet in (and > >>> the speakerphone). I think we better reschedule. How about starting > >>> up > >>> again on Sunday? > >>> > >>> Gregg > >>> > >>> > >>>> -----Original Message----- > >>>> From: Lincoln Stein [mailto:lstein at cshl.edu] > >>>> Sent: Friday, June 24, 2005 2:18 PM > >>>> To: Helt,Gregg > >>>> Cc: das2 at portal.open-bio.org > >>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > >>>> > >>>> Sounds good! > >>>> > >>>> Lincoln > >>>> > >>>> On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: > >>>>> Yep, will that work for you? We're holding it in the Ambassador II > >>> room > >>>>> (where BOSC is), the hotel folks are supposed to install a > >>> speakerphone > >>>>> for us. Same teleconference numbers: > >>>>> Phone: 800-531-3250 > >>>>> Id: 2879055 > >>>>> > >>>>> thanks, > >>>>> gregg > >>>>> > >>>>>> -----Original Message----- > >>>>>> From: das2-bounces at portal.open-bio.org > >>>>> > >>>>> [mailto:das2-bounces at portal.open- > >>>>> > >>>>>> bio.org] On Behalf Of Lincoln Stein > >>>>>> Sent: Friday, June 24, 2005 11:14 AM > >>>>>> To: das2 at portal.open-bio.org > >>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > >>>>>> > >>>>>> Hi, > >>>>>> > >>>>>> Are we still on for a DAS meeting (me by telephone) at 7 pm this > >>>>> > >>>>> evening? > >>>>> > >>>>>> Lincoln > >>>>>> > >>>>>> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: > >>>>>>> late breaking news. > >>>>>>> > >>>>>>> we're meeting at 2 in room c on the 39th flooor. > >>>>>>> > >>>>>>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > >>>>>>>> Still trying to figure out DAS/2 meeting location today, > >>> hoping to > >>>>>>>> start > >>>>>>>> around 1:30 PM. Assuming we have access to a phone, for those > >>> of > >>>>> > >>>>> you > >>>>> > >>>>>>>> who need to call in, here's the conference line info: > >>>>>>>> > >>>>>>>> Dial-in, domestic: 800-531-3250 > >>>>>>>> International: 303-928-2693 > >>>>>>>> Conference ID: 2879055 > >>>>>>>> > >>>>>>>> thanks, > >>>>>>>> gregg > >>>>>>>> > >>>>>>>>> -----Original Message----- > >>>>>>>>> From: das2-bounces at portal.open-bio.org > >>>>>>>> > >>>>>>>> [mailto:das2-bounces at portal.open- > >>>>>>>> > >>>>>>>>> bio.org] On Behalf Of Helt,Gregg > >>>>>>>>> Sent: Thursday, June 23, 2005 11:19 AM > >>>>>>>>> To: Suzanna Lewis > >>>>>>>>> Cc: DAS/2 > >>>>>>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > >>>>>>>>> > >>>>>>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby > >>> (3rd > >>>>>>>> > >>>>>>>> floor) > >>>>>>>> > >>>>>>>>> and figure it out from there. > >>>>>>>>> > >>>>>>>>> gregg > >>>>>>>>> > >>>>>>>>>> -----Original Message----- > >>>>>>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] > >>>>>>>>>> Sent: Thursday, June 23, 2005 7:43 AM > >>>>>>>>>> To: Helt,Gregg > >>>>>>>>>> Cc: DAS/2 > >>>>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > >>>>>>>>>> > >>>>>>>>>> Where? > >>>>>>>>>> > >>>>>>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > >>>>>>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let > >>> me > >>>>>>>> > >>>>>>>> know > >>>>>>>> > >>>>>>>>>>> what > >>>>>>>>>>> you think. > >>>>>>>>>>> > >>>>>>>>>>> gregg > >>>>>>>>>>> > >>>>>>>>>>> Thursday, June 23 > >>>>>>>>>>> 1:30 PM - 3 PM Retrieval Spec > >>>>>>>>>>> 3:30 PM - 5 PM Registry and Discovery > >>>>>>>>>>> 5 PM - 6 PM Writeback Spec > >>>>>>>>>>> 6 PM - 7 PM Continuation Grant > >>>>>>>>>>> 7:00 PM Dinner > >>>>>>>>>>> > >>>>>>>>>>> Friday, June 24 > >>>>>>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? > >>>>>>>>>>> 5 PM -- ?? DAS/2 BOF > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> _______________________________________________ > >>>>>>>>>>> DAS2 mailing list > >>>>>>>>>>> DAS2 at portal.open-bio.org > >>>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > >>>>>>>>> > >>>>>>>>> _______________________________________________ > >>>>>>>>> DAS2 mailing list > >>>>>>>>> DAS2 at portal.open-bio.org > >>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > >>>>>>>> > >>>>>>>> _______________________________________________ > >>>>>>>> DAS2 mailing list > >>>>>>>> DAS2 at portal.open-bio.org > >>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> DAS2 mailing list > >>>>>>> DAS2 at portal.open-bio.org > >>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > >>>>>> > >>>>>> -- > >>>>>> Lincoln Stein > >>>>>> lstein at cshl.edu > >>>>>> Cold Spring Harbor Laboratory > >>>>>> 1 Bungtown Road > >>>>>> Cold Spring Harbor, NY 11724 > >>>>>> (516) 367-8380 (voice) > >>>>>> (516) 367-8389 (fax) > >>>>>> _______________________________________________ > >>>>>> DAS2 mailing list > >>>>>> DAS2 at portal.open-bio.org > >>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > >>>> > >>>> -- > >>>> Lincoln D. Stein > >>>> Cold Spring Harbor Laboratory > >>>> 1 Bungtown Road > >>>> Cold Spring Harbor, NY 11724 > >>> > >>> _______________________________________________ > >>> DAS2 mailing list > >>> DAS2 at portal.open-bio.org > >>> http://portal.open-bio.org/mailman/listinfo/das2 > >> > >> _______________________________________________ > >> DAS2 mailing list > >> DAS2 at portal.open-bio.org > >> http://portal.open-bio.org/mailman/listinfo/das2 > > From lstein at cshl.edu Mon Jun 27 09:33:04 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 27 Jun 2005 09:33:04 -0400 Subject: [DAS2] DAS/2 meeting schedule for Monday In-Reply-To: References: Message-ID: <200506270933.05116.lstein@cshl.edu> Ok, I'll be there. I'm working on the Reactome grant, so I will probably not be able to attend the entire meeting, but I am keenly interested in hearing what the BOF attendees had to say about querying over ontologies. Lincoln On Sunday 26 June 2005 06:35 pm, Helt,Gregg wrote: > I've reserved a room for a DAS/2 meeting tomorrow (Monday), Duluth (on > the 5th floor), from 2PM to 6PM Eastern time. It also comes with a > better speakerphone than what we had last time. Lincoln and Allen, > please let me know as soon as possible if you can't make it! With a > four hour window, I'm hoping you can both teleconference in for at least > part of the meeting. > > I've also tentatively reserved the same room for 2PM to 5 PM Tuesday, > Eastern time. > > Conference phone #: 800-531-3250 > Conference id: 2879055 > > gregg > > > -----Original Message----- > > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > Sent: Sunday, June 26, 2005 11:29 AM > > To: Chervitz, Steve > > Cc: Helt,Gregg; das2 at portal.open-bio.org > > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > > > No meeting today. Gregg will be back latter today to arrange a room > > for > > > tomorrow and let us know. (appears like my last mail didn't get > > through) > > > > On Jun 26, 2005, at 11:26 AM, Chervitz, Steve wrote: > > > Is there a meeting on for today? Did it happen already? Gregg: Are > > you > > > > going > > > to be back at ISMB today? > > > > > > Steve > > > > > >> From: Suzanna Lewis > > >> Date: Fri, 24 Jun 2005 19:56:23 -0400 > > >> To: "Helt,Gregg" > > >> Cc: > > >> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >> > > >> Ah, I was wondering why I didn't find you there. Sunday morn would > > >> work > > >> for me. > > >> > > >> On Jun 24, 2005, at 7:08 PM, Helt,Gregg wrote: > > >>> Apologies, looks like we lost the room I was planning to meet in > > (and > > > >>> the speakerphone). I think we better reschedule. How about > > starting > > > >>> up > > >>> again on Sunday? > > >>> > > >>> Gregg > > >>> > > >>>> -----Original Message----- > > >>>> From: Lincoln Stein [mailto:lstein at cshl.edu] > > >>>> Sent: Friday, June 24, 2005 2:18 PM > > >>>> To: Helt,Gregg > > >>>> Cc: das2 at portal.open-bio.org > > >>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >>>> > > >>>> Sounds good! > > >>>> > > >>>> Lincoln > > >>>> > > >>>> On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: > > >>>>> Yep, will that work for you? We're holding it in the Ambassador > > II > > > >>> room > > >>> > > >>>>> (where BOSC is), the hotel folks are supposed to install a > > >>> > > >>> speakerphone > > >>> > > >>>>> for us. Same teleconference numbers: > > >>>>> Phone: 800-531-3250 > > >>>>> Id: 2879055 > > >>>>> > > >>>>> thanks, > > >>>>> gregg > > >>>>> > > >>>>>> -----Original Message----- > > >>>>>> From: das2-bounces at portal.open-bio.org > > >>>>> > > >>>>> [mailto:das2-bounces at portal.open- > > >>>>> > > >>>>>> bio.org] On Behalf Of Lincoln Stein > > >>>>>> Sent: Friday, June 24, 2005 11:14 AM > > >>>>>> To: das2 at portal.open-bio.org > > >>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >>>>>> > > >>>>>> Hi, > > >>>>>> > > >>>>>> Are we still on for a DAS meeting (me by telephone) at 7 pm > > this > > > >>>>> evening? > > >>>>> > > >>>>>> Lincoln > > >>>>>> > > >>>>>> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: > > >>>>>>> late breaking news. > > >>>>>>> > > >>>>>>> we're meeting at 2 in room c on the 39th flooor. > > >>>>>>> > > >>>>>>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > > >>>>>>>> Still trying to figure out DAS/2 meeting location today, > > >>> > > >>> hoping to > > >>> > > >>>>>>>> start > > >>>>>>>> around 1:30 PM. Assuming we have access to a phone, for > > those > > > >>> of > > >>> > > >>>>> you > > >>>>> > > >>>>>>>> who need to call in, here's the conference line info: > > >>>>>>>> > > >>>>>>>> Dial-in, domestic: 800-531-3250 > > >>>>>>>> International: 303-928-2693 > > >>>>>>>> Conference ID: 2879055 > > >>>>>>>> > > >>>>>>>> thanks, > > >>>>>>>> gregg > > >>>>>>>> > > >>>>>>>>> -----Original Message----- > > >>>>>>>>> From: das2-bounces at portal.open-bio.org > > >>>>>>>> > > >>>>>>>> [mailto:das2-bounces at portal.open- > > >>>>>>>> > > >>>>>>>>> bio.org] On Behalf Of Helt,Gregg > > >>>>>>>>> Sent: Thursday, June 23, 2005 11:19 AM > > >>>>>>>>> To: Suzanna Lewis > > >>>>>>>>> Cc: DAS/2 > > >>>>>>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > > >>>>>>>>> > > >>>>>>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby > > >>> > > >>> (3rd > > >>> > > >>>>>>>> floor) > > >>>>>>>> > > >>>>>>>>> and figure it out from there. > > >>>>>>>>> > > >>>>>>>>> gregg > > >>>>>>>>> > > >>>>>>>>>> -----Original Message----- > > >>>>>>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > >>>>>>>>>> Sent: Thursday, June 23, 2005 7:43 AM > > >>>>>>>>>> To: Helt,Gregg > > >>>>>>>>>> Cc: DAS/2 > > >>>>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >>>>>>>>>> > > >>>>>>>>>> Where? > > >>>>>>>>>> > > >>>>>>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > > >>>>>>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. > > Let > > > >>> me > > >>> > > >>>>>>>> know > > >>>>>>>> > > >>>>>>>>>>> what > > >>>>>>>>>>> you think. > > >>>>>>>>>>> > > >>>>>>>>>>> gregg > > >>>>>>>>>>> > > >>>>>>>>>>> Thursday, June 23 > > >>>>>>>>>>> 1:30 PM - 3 PM Retrieval Spec > > >>>>>>>>>>> 3:30 PM - 5 PM Registry and Discovery > > >>>>>>>>>>> 5 PM - 6 PM Writeback Spec > > >>>>>>>>>>> 6 PM - 7 PM Continuation Grant > > >>>>>>>>>>> 7:00 PM Dinner > > >>>>>>>>>>> > > >>>>>>>>>>> Friday, June 24 > > >>>>>>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? > > >>>>>>>>>>> 5 PM -- ?? DAS/2 BOF > > >>>>>>>>>>> > > >>>>>>>>>>> > > >>>>>>>>>>> _______________________________________________ > > >>>>>>>>>>> DAS2 mailing list > > >>>>>>>>>>> DAS2 at portal.open-bio.org > > >>>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>>>>> > > >>>>>>>>> _______________________________________________ > > >>>>>>>>> DAS2 mailing list > > >>>>>>>>> DAS2 at portal.open-bio.org > > >>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>>>> > > >>>>>>>> _______________________________________________ > > >>>>>>>> DAS2 mailing list > > >>>>>>>> DAS2 at portal.open-bio.org > > >>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>>> > > >>>>>>> _______________________________________________ > > >>>>>>> DAS2 mailing list > > >>>>>>> DAS2 at portal.open-bio.org > > >>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>> > > >>>>>> -- > > >>>>>> Lincoln Stein > > >>>>>> lstein at cshl.edu > > >>>>>> Cold Spring Harbor Laboratory > > >>>>>> 1 Bungtown Road > > >>>>>> Cold Spring Harbor, NY 11724 > > >>>>>> (516) 367-8380 (voice) > > >>>>>> (516) 367-8389 (fax) > > >>>>>> _______________________________________________ > > >>>>>> DAS2 mailing list > > >>>>>> DAS2 at portal.open-bio.org > > >>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>> > > >>>> -- > > >>>> Lincoln D. Stein > > >>>> Cold Spring Harbor Laboratory > > >>>> 1 Bungtown Road > > >>>> Cold Spring Harbor, NY 11724 > > >>> > > >>> _______________________________________________ > > >>> DAS2 mailing list > > >>> DAS2 at portal.open-bio.org > > >>> http://portal.open-bio.org/mailman/listinfo/das2 > > >> > > >> _______________________________________________ > > >> DAS2 mailing list > > >> DAS2 at portal.open-bio.org > > >> http://portal.open-bio.org/mailman/listinfo/das2 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 -- Lincoln Stein lstein at cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From suzi at fruitfly.org Mon Jun 27 09:57:23 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Mon, 27 Jun 2005 09:57:23 -0400 Subject: [DAS2] DAS/2 meeting schedule for Monday In-Reply-To: <200506270933.05116.lstein@cshl.edu> References: <200506270933.05116.lstein@cshl.edu> Message-ID: <83e2755e1eb5a3f5084233173eaf9374@fruitfly.org> Gregg, I'm in the same dilemma. I must work on the Reactome grant (especially since Lincoln just passed it back to me), but I also would like to hear feedback. I will likely be late (sorry). It sure is a good thing we decided to defer until Nov 1! -S On Jun 27, 2005, at 9:33 AM, Lincoln Stein wrote: > Ok, I'll be there. I'm working on the Reactome grant, so I will > probably not > be able to attend the entire meeting, but I am keenly interested in > hearing > what the BOF attendees had to say about querying over ontologies. > > Lincoln > > > On Sunday 26 June 2005 06:35 pm, Helt,Gregg wrote: >> I've reserved a room for a DAS/2 meeting tomorrow (Monday), Duluth (on >> the 5th floor), from 2PM to 6PM Eastern time. It also comes with a >> better speakerphone than what we had last time. Lincoln and Allen, >> please let me know as soon as possible if you can't make it! With a >> four hour window, I'm hoping you can both teleconference in for at >> least >> part of the meeting. >> >> I've also tentatively reserved the same room for 2PM to 5 PM Tuesday, >> Eastern time. >> >> Conference phone #: 800-531-3250 >> Conference id: 2879055 >> >> gregg >> >>> -----Original Message----- >>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >>> Sent: Sunday, June 26, 2005 11:29 AM >>> To: Chervitz, Steve >>> Cc: Helt,Gregg; das2 at portal.open-bio.org >>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>> >>> No meeting today. Gregg will be back latter today to arrange a room >> >> for >> >>> tomorrow and let us know. (appears like my last mail didn't get >>> through) >>> >>> On Jun 26, 2005, at 11:26 AM, Chervitz, Steve wrote: >>>> Is there a meeting on for today? Did it happen already? Gregg: Are >> >> you >> >>>> going >>>> to be back at ISMB today? >>>> >>>> Steve >>>> >>>>> From: Suzanna Lewis >>>>> Date: Fri, 24 Jun 2005 19:56:23 -0400 >>>>> To: "Helt,Gregg" >>>>> Cc: >>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>> >>>>> Ah, I was wondering why I didn't find you there. Sunday morn would >>>>> work >>>>> for me. >>>>> >>>>> On Jun 24, 2005, at 7:08 PM, Helt,Gregg wrote: >>>>>> Apologies, looks like we lost the room I was planning to meet in >> >> (and >> >>>>>> the speakerphone). I think we better reschedule. How about >> >> starting >> >>>>>> up >>>>>> again on Sunday? >>>>>> >>>>>> Gregg >>>>>> >>>>>>> -----Original Message----- >>>>>>> From: Lincoln Stein [mailto:lstein at cshl.edu] >>>>>>> Sent: Friday, June 24, 2005 2:18 PM >>>>>>> To: Helt,Gregg >>>>>>> Cc: das2 at portal.open-bio.org >>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>>> >>>>>>> Sounds good! >>>>>>> >>>>>>> Lincoln >>>>>>> >>>>>>> On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: >>>>>>>> Yep, will that work for you? We're holding it in the Ambassador >> >> II >> >>>>>> room >>>>>> >>>>>>>> (where BOSC is), the hotel folks are supposed to install a >>>>>> >>>>>> speakerphone >>>>>> >>>>>>>> for us. Same teleconference numbers: >>>>>>>> Phone: 800-531-3250 >>>>>>>> Id: 2879055 >>>>>>>> >>>>>>>> thanks, >>>>>>>> gregg >>>>>>>> >>>>>>>>> -----Original Message----- >>>>>>>>> From: das2-bounces at portal.open-bio.org >>>>>>>> >>>>>>>> [mailto:das2-bounces at portal.open- >>>>>>>> >>>>>>>>> bio.org] On Behalf Of Lincoln Stein >>>>>>>>> Sent: Friday, June 24, 2005 11:14 AM >>>>>>>>> To: das2 at portal.open-bio.org >>>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> Are we still on for a DAS meeting (me by telephone) at 7 pm >> >> this >> >>>>>>>> evening? >>>>>>>> >>>>>>>>> Lincoln >>>>>>>>> >>>>>>>>> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: >>>>>>>>>> late breaking news. >>>>>>>>>> >>>>>>>>>> we're meeting at 2 in room c on the 39th flooor. >>>>>>>>>> >>>>>>>>>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: >>>>>>>>>>> Still trying to figure out DAS/2 meeting location today, >>>>>> >>>>>> hoping to >>>>>> >>>>>>>>>>> start >>>>>>>>>>> around 1:30 PM. Assuming we have access to a phone, for >> >> those >> >>>>>> of >>>>>> >>>>>>>> you >>>>>>>> >>>>>>>>>>> who need to call in, here's the conference line info: >>>>>>>>>>> >>>>>>>>>>> Dial-in, domestic: 800-531-3250 >>>>>>>>>>> International: 303-928-2693 >>>>>>>>>>> Conference ID: 2879055 >>>>>>>>>>> >>>>>>>>>>> thanks, >>>>>>>>>>> gregg >>>>>>>>>>> >>>>>>>>>>>> -----Original Message----- >>>>>>>>>>>> From: das2-bounces at portal.open-bio.org >>>>>>>>>>> >>>>>>>>>>> [mailto:das2-bounces at portal.open- >>>>>>>>>>> >>>>>>>>>>>> bio.org] On Behalf Of Helt,Gregg >>>>>>>>>>>> Sent: Thursday, June 23, 2005 11:19 AM >>>>>>>>>>>> To: Suzanna Lewis >>>>>>>>>>>> Cc: DAS/2 >>>>>>>>>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>>>>>> >>>>>>>>>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby >>>>>> >>>>>> (3rd >>>>>> >>>>>>>>>>> floor) >>>>>>>>>>> >>>>>>>>>>>> and figure it out from there. >>>>>>>>>>>> >>>>>>>>>>>> gregg >>>>>>>>>>>> >>>>>>>>>>>>> -----Original Message----- >>>>>>>>>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >>>>>>>>>>>>> Sent: Thursday, June 23, 2005 7:43 AM >>>>>>>>>>>>> To: Helt,Gregg >>>>>>>>>>>>> Cc: DAS/2 >>>>>>>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>>>>>>> >>>>>>>>>>>>> Where? >>>>>>>>>>>>> >>>>>>>>>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: >>>>>>>>>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. >> >> Let >> >>>>>> me >>>>>> >>>>>>>>>>> know >>>>>>>>>>> >>>>>>>>>>>>>> what >>>>>>>>>>>>>> you think. >>>>>>>>>>>>>> >>>>>>>>>>>>>> gregg >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thursday, June 23 >>>>>>>>>>>>>> 1:30 PM - 3 PM Retrieval Spec >>>>>>>>>>>>>> 3:30 PM - 5 PM Registry and Discovery >>>>>>>>>>>>>> 5 PM - 6 PM Writeback Spec >>>>>>>>>>>>>> 6 PM - 7 PM Continuation Grant >>>>>>>>>>>>>> 7:00 PM Dinner >>>>>>>>>>>>>> >>>>>>>>>>>>>> Friday, June 24 >>>>>>>>>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? >>>>>>>>>>>>>> 5 PM -- ?? DAS/2 BOF >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> DAS2 mailing list >>>>>>>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> DAS2 mailing list >>>>>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> DAS2 mailing list >>>>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> DAS2 mailing list >>>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Lincoln Stein >>>>>>>>> lstein at cshl.edu >>>>>>>>> Cold Spring Harbor Laboratory >>>>>>>>> 1 Bungtown Road >>>>>>>>> Cold Spring Harbor, NY 11724 >>>>>>>>> (516) 367-8380 (voice) >>>>>>>>> (516) 367-8389 (fax) >>>>>>>>> _______________________________________________ >>>>>>>>> DAS2 mailing list >>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>> >>>>>>> -- >>>>>>> Lincoln D. Stein >>>>>>> Cold Spring Harbor Laboratory >>>>>>> 1 Bungtown Road >>>>>>> Cold Spring Harbor, NY 11724 >>>>>> >>>>>> _______________________________________________ >>>>>> DAS2 mailing list >>>>>> DAS2 at portal.open-bio.org >>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>> >>>>> _______________________________________________ >>>>> DAS2 mailing list >>>>> DAS2 at portal.open-bio.org >>>>> http://portal.open-bio.org/mailman/listinfo/das2 >> >> _______________________________________________ >> DAS2 mailing list >> DAS2 at portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/das2 > > -- > Lincoln Stein > lstein at cshl.edu > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From bugzilla-daemon at portal.open-bio.org Mon Jun 27 15:51:57 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 27 Jun 2005 15:51:57 -0400 Subject: [DAS2] [Bug 1792] allow 'type's which aren't derived from sofa Message-ID: <200506271951.j5RJpvu6009089@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1792 sac at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From sac at bioperl.org 2005-06-27 15:51 ------- We decided by teleconference during ISMB that types for genome-DAS should be restricted to SO. We should include documentation describing what to do if you want to annotate a type in the genome- DAS space that isn't in SO. Something like "either notify the SO curators to get your term added or point to the most general feature in SO that applies, and place your term of interest in an ontology that extends SO, and point to that via RDF. Here's an example...." ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 16:07:58 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:07:58 -0400 Subject: [DAS2] [Bug 1797] don't need compact formats for non-feature requests Message-ID: <200506282007.j5SK7wQw001094@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1797 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|das2 at portal.open-bio.org |dalke at dalkescientific.com ------- Additional Comments From dalke at dalkescientific.com 2005-06-28 16:07 ------- everyone agrees. Remove references from the spec. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 16:32:49 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:32:49 -0400 Subject: [DAS2] [Bug 1799] server should put server type & version in the HTTP headers Message-ID: <200506282032.j5SKWn8L001476@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1799 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|das2 at portal.open-bio.org |dalke at dalkescientific.com ------- Additional Comments From dalke at dalkescientific.com 2005-06-28 16:32 ------- Everyone agrees. Does the HTTP spec suggest the proper header for this? ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 16:36:26 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:36:26 -0400 Subject: [DAS2] [Bug 1803] indicate that two reference coordinate systems are the same Message-ID: <200506282036.j5SKaQ0u001514@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1803 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|das2 at portal.open-bio.org |lstein at cshl.org ------- Additional Comments From dalke at dalkescientific.com 2005-06-28 16:36 ------- Lincoln says that he worked on this and was surprised that it wasn't in the spec. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 16:10:27 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:10:27 -0400 Subject: [DAS2] [Bug 1798] add a subelement to for type-specific format info Message-ID: <200506282010.j5SKARib001137@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1798 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |DUPLICATE ------- Additional Comments From dalke at dalkescientific.com 2005-06-28 16:10 ------- *** This bug has been marked as a duplicate of 1796 *** ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 16:48:00 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:48:00 -0400 Subject: [DAS2] [Bug 1807] Where do seqids come from? Message-ID: <200506282048.j5SKm0Pf001685@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1807 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|das2 at portal.open-bio.org |dalke at dalkescientific.com ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 16:47:47 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:47:47 -0400 Subject: [DAS2] [Bug 1806] When should DAS/2 URLs end with a '/'? Message-ID: <200506282047.j5SKllH6001677@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1806 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- Additional Comments From dalke at dalkescientific.com 2005-06-28 16:47 ------- The Ren Cen Triumvirate has decided here shall be no terminal '/'s on any DAS/2 URLS, though they may be used in xml:base. So mote it be. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 16:50:02 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:50:02 -0400 Subject: [DAS2] [Bug 1808] , region ids and sequence ids Message-ID: <200506282050.j5SKo2xV001746@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1808 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- Additional Comments From dalke at dalkescientific.com 2005-06-28 16:50 ------- We change id in into "seqid" and merge it with the start/end information to make a new URL. Example ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 16:50:30 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:50:30 -0400 Subject: [DAS2] [Bug 1808] , region ids and sequence ids Message-ID: <200506282050.j5SKoUXW001765@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1808 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|das2 at portal.open-bio.org |lstein at cshl.org Status|ASSIGNED |NEW ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From lstein at cshl.edu Thu Jun 30 13:50:00 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 30 Jun 2005 13:50:00 -0400 Subject: [DAS2] DAS/2 meeting schedule for Monday In-Reply-To: References: Message-ID: <200506301350.00937.lstein@cshl.edu> Hello, I won't be able to participate in today's conference call (if there is one) due to time pressures on getting the Reactome grant out the door. Lincoln On Sunday 26 June 2005 06:35 pm, Helt,Gregg wrote: > I've reserved a room for a DAS/2 meeting tomorrow (Monday), Duluth (on > the 5th floor), from 2PM to 6PM Eastern time. It also comes with a > better speakerphone than what we had last time. Lincoln and Allen, > please let me know as soon as possible if you can't make it! With a > four hour window, I'm hoping you can both teleconference in for at least > part of the meeting. > > I've also tentatively reserved the same room for 2PM to 5 PM Tuesday, > Eastern time. > > Conference phone #: 800-531-3250 > Conference id: 2879055 > > gregg > > > -----Original Message----- > > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > Sent: Sunday, June 26, 2005 11:29 AM > > To: Chervitz, Steve > > Cc: Helt,Gregg; das2 at portal.open-bio.org > > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > > > No meeting today. Gregg will be back latter today to arrange a room > > for > > > tomorrow and let us know. (appears like my last mail didn't get > > through) > > > > On Jun 26, 2005, at 11:26 AM, Chervitz, Steve wrote: > > > Is there a meeting on for today? Did it happen already? Gregg: Are > > you > > > > going > > > to be back at ISMB today? > > > > > > Steve > > > > > >> From: Suzanna Lewis > > >> Date: Fri, 24 Jun 2005 19:56:23 -0400 > > >> To: "Helt,Gregg" > > >> Cc: > > >> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >> > > >> Ah, I was wondering why I didn't find you there. Sunday morn would > > >> work > > >> for me. > > >> > > >> On Jun 24, 2005, at 7:08 PM, Helt,Gregg wrote: > > >>> Apologies, looks like we lost the room I was planning to meet in > > (and > > > >>> the speakerphone). I think we better reschedule. How about > > starting > > > >>> up > > >>> again on Sunday? > > >>> > > >>> Gregg > > >>> > > >>>> -----Original Message----- > > >>>> From: Lincoln Stein [mailto:lstein at cshl.edu] > > >>>> Sent: Friday, June 24, 2005 2:18 PM > > >>>> To: Helt,Gregg > > >>>> Cc: das2 at portal.open-bio.org > > >>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >>>> > > >>>> Sounds good! > > >>>> > > >>>> Lincoln > > >>>> > > >>>> On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: > > >>>>> Yep, will that work for you? We're holding it in the Ambassador > > II > > > >>> room > > >>> > > >>>>> (where BOSC is), the hotel folks are supposed to install a > > >>> > > >>> speakerphone > > >>> > > >>>>> for us. Same teleconference numbers: > > >>>>> Phone: 800-531-3250 > > >>>>> Id: 2879055 > > >>>>> > > >>>>> thanks, > > >>>>> gregg > > >>>>> > > >>>>>> -----Original Message----- > > >>>>>> From: das2-bounces at portal.open-bio.org > > >>>>> > > >>>>> [mailto:das2-bounces at portal.open- > > >>>>> > > >>>>>> bio.org] On Behalf Of Lincoln Stein > > >>>>>> Sent: Friday, June 24, 2005 11:14 AM > > >>>>>> To: das2 at portal.open-bio.org > > >>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >>>>>> > > >>>>>> Hi, > > >>>>>> > > >>>>>> Are we still on for a DAS meeting (me by telephone) at 7 pm > > this > > > >>>>> evening? > > >>>>> > > >>>>>> Lincoln > > >>>>>> > > >>>>>> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: > > >>>>>>> late breaking news. > > >>>>>>> > > >>>>>>> we're meeting at 2 in room c on the 39th flooor. > > >>>>>>> > > >>>>>>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > > >>>>>>>> Still trying to figure out DAS/2 meeting location today, > > >>> > > >>> hoping to > > >>> > > >>>>>>>> start > > >>>>>>>> around 1:30 PM. Assuming we have access to a phone, for > > those > > > >>> of > > >>> > > >>>>> you > > >>>>> > > >>>>>>>> who need to call in, here's the conference line info: > > >>>>>>>> > > >>>>>>>> Dial-in, domestic: 800-531-3250 > > >>>>>>>> International: 303-928-2693 > > >>>>>>>> Conference ID: 2879055 > > >>>>>>>> > > >>>>>>>> thanks, > > >>>>>>>> gregg > > >>>>>>>> > > >>>>>>>>> -----Original Message----- > > >>>>>>>>> From: das2-bounces at portal.open-bio.org > > >>>>>>>> > > >>>>>>>> [mailto:das2-bounces at portal.open- > > >>>>>>>> > > >>>>>>>>> bio.org] On Behalf Of Helt,Gregg > > >>>>>>>>> Sent: Thursday, June 23, 2005 11:19 AM > > >>>>>>>>> To: Suzanna Lewis > > >>>>>>>>> Cc: DAS/2 > > >>>>>>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > > >>>>>>>>> > > >>>>>>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby > > >>> > > >>> (3rd > > >>> > > >>>>>>>> floor) > > >>>>>>>> > > >>>>>>>>> and figure it out from there. > > >>>>>>>>> > > >>>>>>>>> gregg > > >>>>>>>>> > > >>>>>>>>>> -----Original Message----- > > >>>>>>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > >>>>>>>>>> Sent: Thursday, June 23, 2005 7:43 AM > > >>>>>>>>>> To: Helt,Gregg > > >>>>>>>>>> Cc: DAS/2 > > >>>>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >>>>>>>>>> > > >>>>>>>>>> Where? > > >>>>>>>>>> > > >>>>>>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > > >>>>>>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. > > Let > > > >>> me > > >>> > > >>>>>>>> know > > >>>>>>>> > > >>>>>>>>>>> what > > >>>>>>>>>>> you think. > > >>>>>>>>>>> > > >>>>>>>>>>> gregg > > >>>>>>>>>>> > > >>>>>>>>>>> Thursday, June 23 > > >>>>>>>>>>> 1:30 PM - 3 PM Retrieval Spec > > >>>>>>>>>>> 3:30 PM - 5 PM Registry and Discovery > > >>>>>>>>>>> 5 PM - 6 PM Writeback Spec > > >>>>>>>>>>> 6 PM - 7 PM Continuation Grant > > >>>>>>>>>>> 7:00 PM Dinner > > >>>>>>>>>>> > > >>>>>>>>>>> Friday, June 24 > > >>>>>>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? > > >>>>>>>>>>> 5 PM -- ?? DAS/2 BOF > > >>>>>>>>>>> > > >>>>>>>>>>> > > >>>>>>>>>>> _______________________________________________ > > >>>>>>>>>>> DAS2 mailing list > > >>>>>>>>>>> DAS2 at portal.open-bio.org > > >>>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>>>>> > > >>>>>>>>> _______________________________________________ > > >>>>>>>>> DAS2 mailing list > > >>>>>>>>> DAS2 at portal.open-bio.org > > >>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>>>> > > >>>>>>>> _______________________________________________ > > >>>>>>>> DAS2 mailing list > > >>>>>>>> DAS2 at portal.open-bio.org > > >>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>>> > > >>>>>>> _______________________________________________ > > >>>>>>> DAS2 mailing list > > >>>>>>> DAS2 at portal.open-bio.org > > >>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>> > > >>>>>> -- > > >>>>>> Lincoln Stein > > >>>>>> lstein at cshl.edu > > >>>>>> Cold Spring Harbor Laboratory > > >>>>>> 1 Bungtown Road > > >>>>>> Cold Spring Harbor, NY 11724 > > >>>>>> (516) 367-8380 (voice) > > >>>>>> (516) 367-8389 (fax) > > >>>>>> _______________________________________________ > > >>>>>> DAS2 mailing list > > >>>>>> DAS2 at portal.open-bio.org > > >>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>> > > >>>> -- > > >>>> Lincoln D. Stein > > >>>> Cold Spring Harbor Laboratory > > >>>> 1 Bungtown Road > > >>>> Cold Spring Harbor, NY 11724 > > >>> > > >>> _______________________________________________ > > >>> DAS2 mailing list > > >>> DAS2 at portal.open-bio.org > > >>> http://portal.open-bio.org/mailman/listinfo/das2 > > >> > > >> _______________________________________________ > > >> DAS2 mailing list > > >> DAS2 at portal.open-bio.org > > >> http://portal.open-bio.org/mailman/listinfo/das2 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From dalke at dalkescientific.com Fri Jun 3 18:50:47 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 3 Jun 2005 12:50:47 -0600 Subject: [DAS2] structure DAS Message-ID: I've been thinking more about the general idea of a structure DAS. I think it would be good to have someone with more recent (and better) structure knowledge than I do. This may be the woman from RCSB mentioned yesterday. Another idea is Steven Brenner. There are two main ways to think about proteins: sequence and conformation. The sequence model is similar to that used for DNA. Sequences have residues arranged in a line, with positions numbered by position. The biggest database for this is SWISS-PROT. Here's an example of features FT DOMAIN 583 920 HECT. FT REGION 515 571 PABP-like. FT COMPBIAS 108 119 Asp/Glu-rich (acidic). FT COMPBIAS 158 181 Pro-rich. FT COMPBIAS 451 470 Arg/Glu-rich (mixed charge). FT COMPBIAS 479 488 Arg/Asp-rich (mixed charge). FT COMPBIAS 610 621 Asp/Glu-rich (acidic). FT COMPBIAS 858 878 Pro-rich. FT ACT_SITE 889 889 Glycyl thioester intermediate (By FT similarity). These are feature types, start/end position, and a description. I imagine there is an ontology for these but I haven't been following that work. Structure is more complicated. The biggest data source for this is the PDB. Things to worry about: * a PDB record may contain aggregates of protein, DNA, lipids, waters, ions, ligands, post-translational modifications and other bits and pieces. * the sequence listed for a chain may be different than found from crystallography. * residue numbers in the structure may not be consecutive. Eg, in a chain the residue ids may be -2, -1, 1, 2A, 2B, 2C. The numbering is often done to preserve residue identifiers across homologous structures. * some features are at the atomic level and not feature level. For that matter, some people like things like "center of ring" but I think we can ignore those. Others like "binding pocket" but there's no good way to specify that. * some residues have "alternate" conformations, eg, a side chain that's believed to have two common orientations. I don't think we need to worry about this. * NMR structures (and others) may have multiple models. I think we don't need to worry about this. All programs I know of handle these as alternate conformations and have no way to say a given feature is on only one of those conformations. * some features may be over several regions of a protein, or across several different chains. Eg, a disulphide bond between two different proteins or an indicator of a beta barrel composed of multiple proteins * strange things, like a protein covalently bonded to a piece of DNA. Those chemists are so whacky! Here's a picture of one done in my old group http://www.ks.uiuc.edu/Research/pro_DNA/hmgd/SDNA_t.gif from http://www.ks.uiuc.edu/Research/pro_DNA/hmgd/ I think it's okay to linearize these. * crystal structures and symmetries. One example that comes to mind is the virus structure I worked on where a beta sheet went from one protein chain on the given protomer to another protein chain on the next protomer around the 5-fold symmetry access. But the structure record only contains a single protomer. I don't think we need to worry about this because to the best of my knowledge that information is not available in any database; it's extracted by humans reading the comments and associated papers. Beyond the technical details, Who are the test users? What's the reference platform? Should there even be one? There's a boatload of 3d structure viewers. A decade ago Steven Brenner proposed a generic format for selection + annotation information. Perhaps that's a better path? Is writeback needed? Andrew dalke at dalkescientific.com From th at sanger.ac.uk Fri Jun 3 19:31:20 2005 From: th at sanger.ac.uk (Tim Hubbard) Date: Fri, 3 Jun 2005 20:31:20 +0100 Subject: [DAS2] structure DAS In-Reply-To: References: Message-ID: Hi Andrew, We already have a DAS1 enabled structure browser (SPICE - java webstart based on JMol) as part of the efamily project - see here: http://www.efamily.org.uk/software/dasclients/spice/ This gets structure information from a reference DAS1 server that has been extended with a 'structure' command (spits out 3D coordinates as well as sequence). There are various plugins for this server that will server coordinate sets from raw PDB files, a replicated oracle instance of MSD and structures contained in SRS. SPICE can display features from DAS servers on either PDBRESNUM coordinate or UNIPROT coordinate systems. There's an DAS alignment service (another DAS1 extension that we've implemented) that provides the mapping between the two coordinate systems. By default, SPICE gets information about available DAS servers from a DAS server registry that we have setup and are starting to use seriously. The following is the interface for browsing lists, but the registry itself is a webservice that can be called and queried from clients http://das.sanger.ac.uk/registry/listServices.jsp (select name 'UniProt' or 'PDBresnum' to get lists of what services have been registered with this. Both the efamily and Biosapiens projects are using this) This doesn't of course address true 3D DAS (DAS servers that provide 3D points or surfaces wrt to 3D structures) but it does allow us to map sequence features onto structure easily and we'll be building on it. SPICE and the associated DAS extensions have been implemented by Andreas Prlic - with some help from Thomas Down, the developer of Dazzle and others at Sanger. I'm sure they will chime in with details to questions about this. Tim At 12:50 pm -0600 3/6/05, Andrew Dalke wrote: >I've been thinking more about the general idea of a structure DAS. > >I think it would be good to have someone with more recent >(and better) structure knowledge than I do. This may be >the woman from RCSB mentioned yesterday. Another idea is >Steven Brenner. > >There are two main ways to think about proteins: sequence >and conformation. > >The sequence model is similar to that used for DNA. >Sequences have residues arranged in a line, with positions >numbered by position. > >The biggest database for this is SWISS-PROT. Here's >an example of features > >FT DOMAIN 583 920 HECT. >FT REGION 515 571 PABP-like. >FT COMPBIAS 108 119 Asp/Glu-rich (acidic). >FT COMPBIAS 158 181 Pro-rich. >FT COMPBIAS 451 470 Arg/Glu-rich (mixed charge). >FT COMPBIAS 479 488 Arg/Asp-rich (mixed charge). >FT COMPBIAS 610 621 Asp/Glu-rich (acidic). >FT COMPBIAS 858 878 Pro-rich. >FT ACT_SITE 889 889 Glycyl thioester intermediate (By >FT similarity). > >These are feature types, start/end position, and a description. >I imagine there is an ontology for these but I haven't been >following that work. > > >Structure is more complicated. The biggest data source >for this is the PDB. Things to worry about: > > * a PDB record may contain aggregates of protein, DNA, lipids, >waters, ions, ligands, post-translational modifications and >other bits and pieces. > > * the sequence listed for a chain may be different than >found from crystallography. > > * residue numbers in the structure may not be consecutive. Eg, >in a chain the residue ids may be -2, -1, 1, 2A, 2B, 2C. The >numbering is often done to preserve residue identifiers across >homologous structures. > > * some features are at the atomic level and not feature level. >For that matter, some people like things like "center of ring" >but I think we can ignore those. Others like "binding pocket" >but there's no good way to specify that. > > * some residues have "alternate" conformations, eg, a side >chain that's believed to have two common orientations. I >don't think we need to worry about this. > > * NMR structures (and others) may have multiple models. >I think we don't need to worry about this. All programs I >know of handle these as alternate conformations and have >no way to say a given feature is on only one of those >conformations. > > * some features may be over several regions of a protein, >or across several different chains. Eg, a disulphide bond >between two different proteins or an indicator of a beta >barrel composed of multiple proteins > > * strange things, like a protein covalently bonded to a >piece of DNA. Those chemists are so whacky! Here's a >picture of one done in my old group > http://www.ks.uiuc.edu/Research/pro_DNA/hmgd/SDNA_t.gif >from > http://www.ks.uiuc.edu/Research/pro_DNA/hmgd/ >I think it's okay to linearize these. > > * crystal structures and symmetries. One example that >comes to mind is the virus structure I worked on where >a beta sheet went from one protein chain on the given >protomer to another protein chain on the next protomer >around the 5-fold symmetry access. But the structure >record only contains a single protomer. I don't think >we need to worry about this because to the best of >my knowledge that information is not available in >any database; it's extracted by humans reading the >comments and associated papers. > > >Beyond the technical details, > > Who are the test users? > > What's the reference platform? Should there even be one? >There's a boatload of 3d structure viewers. A decade ago >Steven Brenner proposed a generic format for selection + >annotation information. Perhaps that's a better path? > > Is writeback needed? > > Andrew > dalke at dalkescientific.com > >_______________________________________________ >DAS2 mailing list >DAS2 at portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/das2 -- ---------------------------------------------------------------------------- Dr Tim Hubbard email: th at sanger.ac.uk Head of Human Genome Analysis Tel (direct): +44 1223 496886 Wellcome Trust Sanger Institute Tel (switch): +44 1223 834244 Wellcome Trust Genome Campus, Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. UK. URL: http://www.sanger.ac.uk/Users/th ---------------------------------------------------------------------------- From dalke at dalkescientific.com Tue Jun 7 07:32:14 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 7 Jun 2005 01:32:14 -0600 Subject: [DAS2] early dasypus output Message-ID: While at this point its mostly readable only by me, here's an example of the current dasypus validation. As you can see, there are many things to fix in both the current server and the spec. Andrew [Andrew-Dalkes-Computer:~/cvses/dasypus/dasypus] dalke% python dasypus.py ========> client.sources <=============== ERROR Unknown content-type 'text/x-das-source+xml' for service 'sources' WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: Fixing DAS namespace {http://www.biodas.org/ns/das/2.00}SOURCES; should be {http://www.biodas.org/ns/das/genome/2.00}SOURCES WARNING: Fixing base of http://das.biopackages.net:0/das; should be http://das.biopackages.net/das/genome/ Comparing sources with single source ========> client.source <=============== ERROR Unknown content-type 'text/das-source+xml' for service 'source' WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: Fixing DAS namespace {http://www.biodas.org/ns/das/2.00}SOURCES; should be {http://www.biodas.org/ns/das/genome/2.00}SOURCES Different: taxon: 'FIXME' != 'http://www.ncbi.nlm.nih.gov/taxon-browser?id=FIXME' ========> client.detailed_source <=============== ERROR Unknown content-type 'text/x-das-source-details+xml' for service 'detailed_source' WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: VERSION tag not closed WARNING: Fixing DAS namespace {http://www.biodas.org/ns/das/2.00}SOURCE; should be {http://www.biodas.org/ns/das/genome/2.00}SOURCE WARNING: Detailed SOURCE description=='blahblahblah' WARNING: Detailed SOURCE VERSION[0] description=='blahblahblah' ERROR Detailed SOURCE VERSION[0] created=='FIXME, a timestamp' not ISO date ERROR Detailed SOURCE VERSION[0] modified=='FIXME, a timestamp' not ISO date different id 'http://das.biopackages.net/das/genome/chado/chado-Hsa-17' != 'chado' types_url http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing WARNING: TYPES TYPE[1] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[1] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[1] source=="whatever" WARNING: TYPES TYPE[1] uses xml:base; add to the DAS/2 spec ERROR server gives 505 error with '%s'. Removing. WARNING: TYPES TYPE[2] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[2] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[2] source=="whatever" WARNING: TYPES TYPE[2] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[2] id=="SO:five_prime_UTR" is not a valid relative URL; fixing WARNING: TYPES TYPE[3] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[3] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[3] source=="whatever" WARNING: TYPES TYPE[3] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[3] id=="SO:gene_part" is not a valid relative URL; fixing WARNING: TYPES TYPE[4] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[4] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[4] source=="whatever" WARNING: TYPES TYPE[4] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[4] id=="SO:located_sequence_feature" is not a valid relative URL; fixing WARNING: TYPES TYPE[5] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[5] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[5] source=="whatever" WARNING: TYPES TYPE[5] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[5] id=="SO:mature_peptide" is not a valid relative URL; fixing WARNING: TYPES TYPE[6] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[6] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[6] source=="whatever" WARNING: TYPES TYPE[6] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[6] id=="SO:mRNA" is not a valid relative URL; fixing WARNING: TYPES TYPE[7] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[7] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[7] source=="whatever" WARNING: TYPES TYPE[7] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[7] id=="SO:PCR_product" is not a valid relative URL; fixing WARNING: TYPES TYPE[8] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[8] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[8] source=="whatever" WARNING: TYPES TYPE[8] uses xml:base; add to the DAS/2 spec ERROR server gives 505 error with '%s'. Removing. WARNING: TYPES TYPE[9] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[9] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[9] source=="whatever" WARNING: TYPES TYPE[9] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[9] id=="SO:polypeptide" is not a valid relative URL; fixing WARNING: TYPES TYPE[10] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[10] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[10] source=="whatever" WARNING: TYPES TYPE[10] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[10] id=="SO:primary_transcript" is not a valid relative URL; fixing WARNING: TYPES TYPE[11] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[11] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[11] source=="whatever" WARNING: TYPES TYPE[11] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[11] id=="SO:processed_transcript" is not a valid relative URL; fixing WARNING: TYPES TYPE[12] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[12] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[12] source=="whatever" WARNING: TYPES TYPE[12] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[12] id=="SO:reagent" is not a valid relative URL; fixing WARNING: TYPES TYPE[13] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[13] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[13] source=="whatever" WARNING: TYPES TYPE[13] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[13] id=="SO:region" is not a valid relative URL; fixing WARNING: TYPES TYPE[14] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[14] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[14] source=="whatever" WARNING: TYPES TYPE[14] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[14] id=="SO:SNP" is not a valid relative URL; fixing WARNING: TYPES TYPE[15] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[15] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[15] source=="whatever" WARNING: TYPES TYPE[15] uses xml:base; add to the DAS/2 spec ERROR server gives 505 error with '%s'. Removing. WARNING: TYPES TYPE[16] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[16] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[16] source=="whatever" WARNING: TYPES TYPE[16] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[16] id=="SO:three_prime_UTR" is not a valid relative URL; fixing WARNING: TYPES TYPE[17] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[17] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[17] source=="whatever" WARNING: TYPES TYPE[17] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[17] id=="SO:transcript" is not a valid relative URL; fixing WARNING: TYPES TYPE[18] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[18] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[18] source=="whatever" WARNING: TYPES TYPE[18] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[18] id=="SO:UTR" is not a valid relative URL; fixing WARNING: TYPES TYPE[19] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[19] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[19] source=="whatever" WARNING: TYPES TYPE[19] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[19] id=="SO:protein" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:CDS WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: five_prime_UTR WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:five_prime_UTR" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: gene_part WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:gene_part" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: located_sequence_feature WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:located_sequence_feature" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: mature_peptide WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:mature_peptide" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:mRNA WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:mRNA" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: PCR_product WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:PCR_product" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: polypeptide WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:polypeptide" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: primary_transcript WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:primary_transcript" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: processed_transcript WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:processed_transcript" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: reagent WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:reagent" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:region WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:region" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:SNP WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:SNP" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: three_prime_UTR WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:three_prime_UTR" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: transcript WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:transcript" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:UTR WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:UTR" is not a valid relative URL; fixing Trying http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: protein WARNING: Adding X-DAS-Server header 'gmod/0.0' WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 spec WARNING: TYPES TYPE[0] source=="whatever" WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec ERROR TYPES TYPE[0] id=="SO:protein" is not a valid relative URL; fixing [Andrew-Dalkes-Computer:~/cvses/dasypus/dasypus] dalke% Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Tue Jun 7 07:38:39 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 7 Jun 2005 01:38:39 -0600 Subject: [DAS2] squid proxy Message-ID: <2af3af7d3d958611b8d282682efd584b@dalkescientific.com> P.S. Development was much more fun once I set up a Squid proxy for the dev. server and forced it to cache everything for up to a day. Besides getting rid of the network overhead, some of the server responses (like 'type') take a noticeable time. In doing that I found a bug in dasypus. The HTTP request object changes when using a server, so http://www.biodas.org/blah becomes (in effect) http://proxy/http://www.biodas.org/blah Some of my fixups and tests are server-specific and I didn't expect the request server name to change from underneath me. Andrew dalke at dalkescientific.com From allenday at ucla.edu Tue Jun 7 07:53:44 2005 From: allenday at ucla.edu (Allen Day) Date: Tue, 7 Jun 2005 00:53:44 -0700 (PDT) Subject: [DAS2] early dasypus output In-Reply-To: References: Message-ID: This is very helpful. I'm updating the test server tonight, have a look again in a few hours. -Allen On Tue, 7 Jun 2005, Andrew Dalke wrote: > While at this point its mostly readable only by me, here's an example > of the current dasypus validation. > > As you can see, there are many things to fix in both the current > server and the spec. > > Andrew > > > [Andrew-Dalkes-Computer:~/cvses/dasypus/dasypus] dalke% python > dasypus.py > ========> client.sources <=============== > > > ERROR Unknown content-type 'text/x-das-source+xml' for service 'sources' > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: Fixing DAS namespace > {http://www.biodas.org/ns/das/2.00}SOURCES; should be > {http://www.biodas.org/ns/das/genome/2.00}SOURCES > WARNING: Fixing base of http://das.biopackages.net:0/das; should be > http://das.biopackages.net/das/genome/ > Comparing sources with single source > ========> client.source <=============== > > > ERROR Unknown content-type 'text/das-source+xml' for service 'source' > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: Fixing DAS namespace > {http://www.biodas.org/ns/das/2.00}SOURCES; should be > {http://www.biodas.org/ns/das/genome/2.00}SOURCES > Different: > taxon: 'FIXME' != 'http://www.ncbi.nlm.nih.gov/taxon-browser?id=FIXME' > ========> client.detailed_source <=============== > > > ERROR Unknown content-type 'text/x-das-source-details+xml' for service > 'detailed_source' > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: VERSION tag not closed > WARNING: Fixing DAS namespace > {http://www.biodas.org/ns/das/2.00}SOURCE; should be > {http://www.biodas.org/ns/das/genome/2.00}SOURCE > WARNING: Detailed SOURCE description=='blahblahblah' > WARNING: Detailed SOURCE VERSION[0] description=='blahblahblah' > ERROR Detailed SOURCE VERSION[0] created=='FIXME, a timestamp' not ISO > date > ERROR Detailed SOURCE VERSION[0] modified=='FIXME, a timestamp' not ISO > date > different id > 'http://das.biopackages.net/das/genome/chado/chado-Hsa-17' != 'chado' > types_url http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing > WARNING: TYPES TYPE[1] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[1] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[1] source=="whatever" > WARNING: TYPES TYPE[1] uses xml:base; add to the DAS/2 spec > ERROR server gives 505 error with '%s'. Removing. > WARNING: TYPES TYPE[2] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[2] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[2] source=="whatever" > WARNING: TYPES TYPE[2] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[2] id=="SO:five_prime_UTR" is not a valid relative > URL; fixing > WARNING: TYPES TYPE[3] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[3] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[3] source=="whatever" > WARNING: TYPES TYPE[3] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[3] id=="SO:gene_part" is not a valid relative URL; > fixing > WARNING: TYPES TYPE[4] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[4] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[4] source=="whatever" > WARNING: TYPES TYPE[4] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[4] id=="SO:located_sequence_feature" is not a valid > relative URL; fixing > WARNING: TYPES TYPE[5] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[5] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[5] source=="whatever" > WARNING: TYPES TYPE[5] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[5] id=="SO:mature_peptide" is not a valid relative > URL; fixing > WARNING: TYPES TYPE[6] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[6] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[6] source=="whatever" > WARNING: TYPES TYPE[6] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[6] id=="SO:mRNA" is not a valid relative URL; fixing > WARNING: TYPES TYPE[7] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[7] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[7] source=="whatever" > WARNING: TYPES TYPE[7] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[7] id=="SO:PCR_product" is not a valid relative URL; > fixing > WARNING: TYPES TYPE[8] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[8] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[8] source=="whatever" > WARNING: TYPES TYPE[8] uses xml:base; add to the DAS/2 spec > ERROR server gives 505 error with '%s'. Removing. > WARNING: TYPES TYPE[9] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[9] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[9] source=="whatever" > WARNING: TYPES TYPE[9] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[9] id=="SO:polypeptide" is not a valid relative URL; > fixing > WARNING: TYPES TYPE[10] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[10] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[10] source=="whatever" > WARNING: TYPES TYPE[10] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[10] id=="SO:primary_transcript" is not a valid > relative URL; fixing > WARNING: TYPES TYPE[11] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[11] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[11] source=="whatever" > WARNING: TYPES TYPE[11] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[11] id=="SO:processed_transcript" is not a valid > relative URL; fixing > WARNING: TYPES TYPE[12] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[12] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[12] source=="whatever" > WARNING: TYPES TYPE[12] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[12] id=="SO:reagent" is not a valid relative URL; > fixing > WARNING: TYPES TYPE[13] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[13] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[13] source=="whatever" > WARNING: TYPES TYPE[13] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[13] id=="SO:region" is not a valid relative URL; fixing > WARNING: TYPES TYPE[14] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[14] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[14] source=="whatever" > WARNING: TYPES TYPE[14] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[14] id=="SO:SNP" is not a valid relative URL; fixing > WARNING: TYPES TYPE[15] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[15] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[15] source=="whatever" > WARNING: TYPES TYPE[15] uses xml:base; add to the DAS/2 spec > ERROR server gives 505 error with '%s'. Removing. > WARNING: TYPES TYPE[16] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[16] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[16] source=="whatever" > WARNING: TYPES TYPE[16] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[16] id=="SO:three_prime_UTR" is not a valid relative > URL; fixing > WARNING: TYPES TYPE[17] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[17] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[17] source=="whatever" > WARNING: TYPES TYPE[17] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[17] id=="SO:transcript" is not a valid relative URL; > fixing > WARNING: TYPES TYPE[18] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[18] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[18] source=="whatever" > WARNING: TYPES TYPE[18] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[18] id=="SO:UTR" is not a valid relative URL; fixing > WARNING: TYPES TYPE[19] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[19] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[19] source=="whatever" > WARNING: TYPES TYPE[19] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[19] id=="SO:protein" is not a valid relative URL; > fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:CDS > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > five_prime_UTR > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:five_prime_UTR" is not a valid relative > URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > gene_part > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:gene_part" is not a valid relative URL; > fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > located_sequence_feature > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:located_sequence_feature" is not a valid > relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > mature_peptide > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:mature_peptide" is not a valid relative > URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:mRNA > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:mRNA" is not a valid relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > PCR_product > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:PCR_product" is not a valid relative URL; > fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > polypeptide > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:polypeptide" is not a valid relative URL; > fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > primary_transcript > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:primary_transcript" is not a valid relative > URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > processed_transcript > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:processed_transcript" is not a valid > relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > reagent > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:reagent" is not a valid relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:region > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:region" is not a valid relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:SNP > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:SNP" is not a valid relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > three_prime_UTR > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:three_prime_UTR" is not a valid relative > URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > transcript > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:transcript" is not a valid relative URL; > fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:UTR > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:UTR" is not a valid relative URL; fixing > Trying > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > protein > WARNING: Adding X-DAS-Server header 'gmod/0.0' > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > spec > WARNING: TYPES TYPE[0] source=="whatever" > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > ERROR TYPES TYPE[0] id=="SO:protein" is not a valid relative URL; fixing > [Andrew-Dalkes-Computer:~/cvses/dasypus/dasypus] dalke% > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 > From allenday at ucla.edu Tue Jun 7 08:06:43 2005 From: allenday at ucla.edu (Allen Day) Date: Tue, 7 Jun 2005 01:06:43 -0700 (PDT) Subject: [DAS2] early dasypus output In-Reply-To: References: Message-ID: Okay, new code is up. I believe I have fixed the bug from below > > ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing as well as > > WARNING: VERSION tag not closed > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > {http://www.biodas.org/ns/das/2.00}SOURCES; should be -Allen On Tue, 7 Jun 2005, Allen Day wrote: > This is very helpful. I'm updating the test server tonight, have a look > again in a few hours. > > -Allen > > On Tue, 7 Jun 2005, Andrew Dalke wrote: > > > While at this point its mostly readable only by me, here's an example > > of the current dasypus validation. > > > > As you can see, there are many things to fix in both the current > > server and the spec. > > > > Andrew > > > > > > [Andrew-Dalkes-Computer:~/cvses/dasypus/dasypus] dalke% python > > dasypus.py > > ========> client.sources <=============== > > > > > > ERROR Unknown content-type 'text/x-das-source+xml' for service 'sources' > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: Fixing DAS namespace > > {http://www.biodas.org/ns/das/2.00}SOURCES; should be > > {http://www.biodas.org/ns/das/genome/2.00}SOURCES > > WARNING: Fixing base of http://das.biopackages.net:0/das; should be > > http://das.biopackages.net/das/genome/ > > Comparing sources with single source > > ========> client.source <=============== > > > > > > ERROR Unknown content-type 'text/das-source+xml' for service 'source' > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: Fixing DAS namespace > > {http://www.biodas.org/ns/das/2.00}SOURCES; should be > > {http://www.biodas.org/ns/das/genome/2.00}SOURCES > > Different: > > taxon: 'FIXME' != 'http://www.ncbi.nlm.nih.gov/taxon-browser?id=FIXME' > > ========> client.detailed_source <=============== > > > > > > ERROR Unknown content-type 'text/x-das-source-details+xml' for service > > 'detailed_source' > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: VERSION tag not closed > > WARNING: Fixing DAS namespace > > {http://www.biodas.org/ns/das/2.00}SOURCE; should be > > {http://www.biodas.org/ns/das/genome/2.00}SOURCE > > WARNING: Detailed SOURCE description=='blahblahblah' > > WARNING: Detailed SOURCE VERSION[0] description=='blahblahblah' > > ERROR Detailed SOURCE VERSION[0] created=='FIXME, a timestamp' not ISO > > date > > ERROR Detailed SOURCE VERSION[0] modified=='FIXME, a timestamp' not ISO > > date > > different id > > 'http://das.biopackages.net/das/genome/chado/chado-Hsa-17' != 'chado' > > types_url http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing > > WARNING: TYPES TYPE[1] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[1] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[1] source=="whatever" > > WARNING: TYPES TYPE[1] uses xml:base; add to the DAS/2 spec > > ERROR server gives 505 error with '%s'. Removing. > > WARNING: TYPES TYPE[2] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[2] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[2] source=="whatever" > > WARNING: TYPES TYPE[2] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[2] id=="SO:five_prime_UTR" is not a valid relative > > URL; fixing > > WARNING: TYPES TYPE[3] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[3] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[3] source=="whatever" > > WARNING: TYPES TYPE[3] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[3] id=="SO:gene_part" is not a valid relative URL; > > fixing > > WARNING: TYPES TYPE[4] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[4] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[4] source=="whatever" > > WARNING: TYPES TYPE[4] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[4] id=="SO:located_sequence_feature" is not a valid > > relative URL; fixing > > WARNING: TYPES TYPE[5] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[5] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[5] source=="whatever" > > WARNING: TYPES TYPE[5] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[5] id=="SO:mature_peptide" is not a valid relative > > URL; fixing > > WARNING: TYPES TYPE[6] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[6] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[6] source=="whatever" > > WARNING: TYPES TYPE[6] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[6] id=="SO:mRNA" is not a valid relative URL; fixing > > WARNING: TYPES TYPE[7] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[7] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[7] source=="whatever" > > WARNING: TYPES TYPE[7] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[7] id=="SO:PCR_product" is not a valid relative URL; > > fixing > > WARNING: TYPES TYPE[8] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[8] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[8] source=="whatever" > > WARNING: TYPES TYPE[8] uses xml:base; add to the DAS/2 spec > > ERROR server gives 505 error with '%s'. Removing. > > WARNING: TYPES TYPE[9] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[9] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[9] source=="whatever" > > WARNING: TYPES TYPE[9] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[9] id=="SO:polypeptide" is not a valid relative URL; > > fixing > > WARNING: TYPES TYPE[10] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[10] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[10] source=="whatever" > > WARNING: TYPES TYPE[10] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[10] id=="SO:primary_transcript" is not a valid > > relative URL; fixing > > WARNING: TYPES TYPE[11] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[11] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[11] source=="whatever" > > WARNING: TYPES TYPE[11] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[11] id=="SO:processed_transcript" is not a valid > > relative URL; fixing > > WARNING: TYPES TYPE[12] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[12] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[12] source=="whatever" > > WARNING: TYPES TYPE[12] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[12] id=="SO:reagent" is not a valid relative URL; > > fixing > > WARNING: TYPES TYPE[13] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[13] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[13] source=="whatever" > > WARNING: TYPES TYPE[13] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[13] id=="SO:region" is not a valid relative URL; fixing > > WARNING: TYPES TYPE[14] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[14] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[14] source=="whatever" > > WARNING: TYPES TYPE[14] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[14] id=="SO:SNP" is not a valid relative URL; fixing > > WARNING: TYPES TYPE[15] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[15] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[15] source=="whatever" > > WARNING: TYPES TYPE[15] uses xml:base; add to the DAS/2 spec > > ERROR server gives 505 error with '%s'. Removing. > > WARNING: TYPES TYPE[16] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[16] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[16] source=="whatever" > > WARNING: TYPES TYPE[16] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[16] id=="SO:three_prime_UTR" is not a valid relative > > URL; fixing > > WARNING: TYPES TYPE[17] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[17] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[17] source=="whatever" > > WARNING: TYPES TYPE[17] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[17] id=="SO:transcript" is not a valid relative URL; > > fixing > > WARNING: TYPES TYPE[18] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[18] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[18] source=="whatever" > > WARNING: TYPES TYPE[18] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[18] id=="SO:UTR" is not a valid relative URL; fixing > > WARNING: TYPES TYPE[19] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[19] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[19] source=="whatever" > > WARNING: TYPES TYPE[19] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[19] id=="SO:protein" is not a valid relative URL; > > fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:CDS > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > five_prime_UTR > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:five_prime_UTR" is not a valid relative > > URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > gene_part > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:gene_part" is not a valid relative URL; > > fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > located_sequence_feature > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:located_sequence_feature" is not a valid > > relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > mature_peptide > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:mature_peptide" is not a valid relative > > URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:mRNA > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:mRNA" is not a valid relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > PCR_product > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:PCR_product" is not a valid relative URL; > > fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > polypeptide > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:polypeptide" is not a valid relative URL; > > fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > primary_transcript > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:primary_transcript" is not a valid relative > > URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > processed_transcript > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:processed_transcript" is not a valid > > relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > reagent > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:reagent" is not a valid relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:region > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:region" is not a valid relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:SNP > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:SNP" is not a valid relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > three_prime_UTR > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:three_prime_UTR" is not a valid relative > > URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > transcript > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:transcript" is not a valid relative URL; > > fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:UTR > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:UTR" is not a valid relative URL; fixing > > Trying > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: > > protein > > WARNING: Adding X-DAS-Server header 'gmod/0.0' > > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec > > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2 > > spec > > WARNING: TYPES TYPE[0] source=="whatever" > > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec > > ERROR TYPES TYPE[0] id=="SO:protein" is not a valid relative URL; fixing > > [Andrew-Dalkes-Computer:~/cvses/dasypus/dasypus] dalke% > > > > Andrew > > dalke at dalkescientific.com > > > > _______________________________________________ > > DAS2 mailing list > > DAS2 at portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/das2 > > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 > From allenday at ucla.edu Tue Jun 7 09:46:16 2005 From: allenday at ucla.edu (Allen Day) Date: Tue, 7 Jun 2005 02:46:16 -0700 (PDT) Subject: [DAS2] /das/assay namespace Message-ID: is available for browsing on the prototype server. example queries: http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/algorithm http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/assay http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/material http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification These are more interesting: #get quantification 2753. it's a netCDF file of a HG-U133A chip #quantified/normalized with Bioconductor's GCRMA algorithm http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification/2753 #as above, but use a feature filter from genome-das to only retrieve #measurements from 10-90Mb on chrY. http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification/2753?feature.overlaps=chrY/10000000:90000000;algorithm=3 #as above, but retrieve 10-90Mb on chrY for all GCRMA-processed chips, of #which there are 661. http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification?feature.overlaps=chrY/10000000:90000000;algorithm=3 #as above, but restrict to CNS samples instead of all 661. this #filter doesn't work yet. http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification?feature.overlaps=chrY/10000000:90000000;algorithm=3;material.type=MA:central_nervous_system In principle, any feature filter can be used with the /quantification request by simply prefixing with "feature." to enable passthru to the feature filter classes on the server. In practice, none of the Affymetrix probesets are annotated with anything beyond their region and primary type of SO:PCR_product, so the only interesting filters to use deal with coordinates. It could be interesting to start attaching the Affymetrix probeset annotations from NetAffx, so you could e.g. retrieve genome-wide expression of RTKs for all CNS samples, without having to perform overlap queries to get to the annotations on the mRNA that are being assayed... I'm almost happy with my prototype -- I'll turn it into a spec document soon. -Allen From suzi at fruitfly.org Tue Jun 7 16:03:03 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Tue, 7 Jun 2005 09:03:03 -0700 Subject: [DAS2] [Bug 1803] New: indicate that two reference coordinate systems are the same In-Reply-To: <200505261857.j4QIvUYJ014139@portal.open-bio.org> References: <200505261857.j4QIvUYJ014139@portal.open-bio.org> Message-ID: <5c036e8a7297ef59d9df9dd6678e758e@fruitfly.org> A globally unique something would certainly be essential. Has this already gotten settled? On May 26, 2005, at 11:57 AM, bugzilla-daemon at portal.open-bio.org wrote: > http://bugzilla.open-bio.org/show_bug.cgi?id=1803 > > Summary: indicate that two reference coordinate systems are > the > same > Product: BioDAS > Version: 2 > Platform: All > OS/Version: All > Status: NEW > Severity: normal > Priority: P2 > Component: Spec - GET Requests > AssignedTo: das2 at portal.open-bio.org > ReportedBy: dalke at dalkescientific.com > > > If two different servers use the same coordinate system (eg, both > using the same > assembly), is there any way that a client can figure that out? > > Perhaps a server could use a globally unique name, with the agreement > that > the same name is used only if the given regions/* are identical? > > > > ------- You are receiving this mail because: ------- > You are the assignee for the bug, or are watching the assignee. > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From dalke at dalkescientific.com Thu Jun 9 19:58:38 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Thu, 9 Jun 2005 13:58:38 -0600 Subject: [DAS2] das2 spec CVS tagged Message-ID: As we just talked about, I tagged the CVS das/das2 tree with cvs tag -R -c das2-d1 The plan is that the server, client and validator work with that spec version (and its flaws), but we are free to update CVS as needed. At BOSC/ISMB we'll work on updating the spec and writing the renewal grant. Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Fri Jun 10 08:12:28 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 10 Jun 2005 02:12:28 -0600 Subject: [DAS2] latested dasypus checked in Message-ID: <968b6f54fdd5d8491f7d82e066fa92ba@dalkescientific.com> This evening I added checks for: - better reporting of where two data structures differ - tests for region/ - a simple test for sequence/ - workarounds for some gmod problems like (Should be "REGIONS" and should not have "http://http://") The architecture is holding up. There were a few places where I needed to make stronger checks but the core das2 client API hasn't changed. Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Fri Jun 10 08:30:44 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 10 Jun 2005 02:30:44 -0600 Subject: [DAS2] how to test features? Message-ID: What's the appropriate way to test features on a server where I don't know what's present? What I did with DAS/1 was search a range of a certain size and keep shifting the search range until I find something. I would like to improve on that. For example, I know all of the types in the system so I can do a type query and double-check that all the returned features have that type. There's a good chance I'll have some enormous results lists if I do that. Some queries may end up sucking up large chunks of the database. I was thinking that a "limit" option might be useful. For example, "up to 1000 features in the range 1M to 2M." 'Course then the server may need to report "returned 1000 features but 234234 matched the query." Perhaps a server may wish to enforce a max limit on the number of features even if not specified in the request? Eg, for "http://.../features/". If there is a limit, would the number be accessible by the client? Would the spec state a lower bound for what a server must support? If the number of hits is just barely over the limit, what's the right way for the client to get the remaining list of features? Andrew dalke at dalkescientific.com From allenday at ucla.edu Fri Jun 10 10:18:00 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 10 Jun 2005 03:18:00 -0700 (PDT) Subject: [DAS2] latested dasypus checked in In-Reply-To: <968b6f54fdd5d8491f7d82e066fa92ba@dalkescientific.com> References: <968b6f54fdd5d8491f7d82e066fa92ba@dalkescientific.com> Message-ID: On Fri, 10 Jun 2005, Andrew Dalke wrote: > This evening I added checks for: > > - better reporting of where two data structures differ > - tests for region/ > - a simple test for sequence/ > - workarounds for some gmod problems like > > xmlns="http://www.biodas.org/ns/das/genome/2.00" > xmlns:xlink="http://www.w3.org/1999/xlink" > > xml:base="http://http://radius.genomics.ctrl.ucla.edu/das/genome/chado/ > chado-Hsa-17/region/"> > > > (Should be "REGIONS" and should not have "http://http://") just fixed this one on the live server. > > The architecture is holding up. There were a few places > where I needed to make stronger checks but the core das2 > client API hasn't changed. > > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 > From ALoraine at ms.soph.uab.edu Fri Jun 10 14:23:27 2005 From: ALoraine at ms.soph.uab.edu (Ann Loraine) Date: Fri, 10 Jun 2005 09:23:27 -0500 Subject: [DAS2] how to test features? Message-ID: <4E4693F3D36946479044A8997EB05BD201EFE91E@phealth4.sophad.local> If you go with a limit option, you might also consider a sorting option as well. This would be useful to select high-scoring blast hits, for instance. Limits and sorting would also be useful for an analysis DAS spec. -Ann -----Original Message----- From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open-bio.org] On Behalf Of Andrew Dalke Sent: Friday, June 10, 2005 3:31 AM To: DAS/2 Subject: [DAS2] how to test features? What's the appropriate way to test features on a server where I don't know what's present? What I did with DAS/1 was search a range of a certain size and keep shifting the search range until I find something. I would like to improve on that. For example, I know all of the types in the system so I can do a type query and double-check that all the returned features have that type. There's a good chance I'll have some enormous results lists if I do that. Some queries may end up sucking up large chunks of the database. I was thinking that a "limit" option might be useful. For example, "up to 1000 features in the range 1M to 2M." 'Course then the server may need to report "returned 1000 features but 234234 matched the query." Perhaps a server may wish to enforce a max limit on the number of features even if not specified in the request? Eg, for "http://.../features/". If there is a limit, would the number be accessible by the client? Would the spec state a lower bound for what a server must support? If the number of hits is just barely over the limit, what's the right way for the client to get the remaining list of features? Andrew dalke at dalkescientific.com _______________________________________________ DAS2 mailing list DAS2 at portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/das2 From Gregg_Helt at affymetrix.com Fri Jun 10 16:41:11 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Fri, 10 Jun 2005 09:41:11 -0700 Subject: [DAS2] how to test features? Message-ID: In DAS/1 the types response can optionally include a count of the number of features available for that particular type and source. I do think this would be a useful feature to preserve in DAS/2. From that information a client/validator could potentially tune its requested range to return on average a desired number of features. I don't think a server should return only some of the features that meet the search criteria -- should return either all or none. If a server decides that a client is requesting too much data, I think servers should be able to return some sort of "returned feature count too large" error code response. And maybe in the source or versioned source response xml have an optional indication of how many features a server is willing to serve up in a single request, so clients can know this limit in advance. gregg > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Andrew Dalke > Sent: Friday, June 10, 2005 1:31 AM > To: DAS/2 > Subject: [DAS2] how to test features? > > What's the appropriate way to test features on a > server where I don't know what's present? > > What I did with DAS/1 was search a range of a > certain size and keep shifting the search range > until I find something. > > I would like to improve on that. For example, I know > all of the types in the system so I can do a type > query and double-check that all the returned features > have that type. > > There's a good chance I'll have some enormous > results lists if I do that. Some queries may end > up sucking up large chunks of the database. > > I was thinking that a "limit" option might be useful. > For example, "up to 1000 features in the range 1M to > 2M." 'Course then the server may need to report > "returned 1000 features but 234234 matched the query." > > Perhaps a server may wish to enforce a max limit > on the number of features even if not specified in > the request? Eg, for "http://.../features/". > > If there is a limit, would the number be accessible > by the client? Would the spec state a lower bound > for what a server must support? If the number of > hits is just barely over the limit, what's the right > way for the client to get the remaining list of features? > > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From dalke at dalkescientific.com Fri Jun 10 17:13:36 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 10 Jun 2005 11:13:36 -0600 Subject: [DAS2] how to test features? In-Reply-To: References: Message-ID: <171bc94b2a23d784ad5d3dc0acf34d53@dalkescientific.com> Gregg: > In DAS/1 the types response can optionally include a count of the > number > of features available for that particular type and source. I do think > this would be a useful feature to preserve in DAS/2. I don't think it would work that well. Given the way we've structured things it's possible the type/ hierarchy is shared by several feature/ hierarchies. My two mental models are: - a single server where different source/versions shares the same types/ - a server which uses someone else's types/ and regions/ as the reference, adding only features/ > From that > information a client/validator could potentially tune its requested > range to return on average a desired number of features. My shot-in-the-dark guess is that the non-uniform distribution of features lessens its usefulness. > I don't think a server should return only some of the features that > meet > the search criteria -- should return either all or none. If a server > decides that a client is requesting too much data, I think servers > should be able to return some sort of "returned feature count too > large" > error code response. I can go along with that, though I would like to know what a client is supposed to do if it gets that response and if we should specify that a server should be able to return at least (say) 10,000 features at a time. > And maybe in the source or versioned source > response xml have an optional indication of how many features a server > is willing to serve up in a single request, so clients can know this > limit in advance. In thinking some more about that - what would a client do with that information? Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Fri Jun 10 17:52:36 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 10 Jun 2005 11:52:36 -0600 Subject: [DAS2] how to test features? In-Reply-To: References: Message-ID: Ann: > If you go with a limit option, you might also consider including an > sorting option, as well. > > This would be useful to screen out low-scoring blast hits, for > instance. That makes the interface a lot more complicated because the sort order can be different than the request. Eg, "all X sorted by Y". Even worse, it could be "sorted by Y (collated as strings) and break ties by reverse order of Z (collated as numbers)." A thick client could still implement the sort of course, though at the cost of higher overhead. One proposal I made years ago was a two-part request, the first to get a list of feature identifiers, the second to get the information about a feature. That is, /feature?whatever returns The client would then figure out "Oh, I already have A2 and B so I only need to fetch A1 and A3." Then turn around do a bunch of GET requests for the missing fields. One problem with it is that to get high performance requires using HTTP/1.1 pipelining. (Another possibility is a special API to fetch a bunch of features given its URL id, but something feels wrong about it; don't know why though.) I mention it now because the feature hitlist would be relatively small even if all features are returned; there's about 10 extra bytes per name and it compresses well. But that need for pipelining is a big limitation. I don't know if it can be done even in the Python libraries I'm used to. I think it can, I'm just not sure. I don't have the experience, and there's the extra requirement for perl and java client/server support. It wouldn't help the sort problem though, except by downloading everything into the client. Andrew dalke at dalkescientific.com From Gregg_Helt at affymetrix.com Fri Jun 10 19:27:06 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Fri, 10 Jun 2005 12:27:06 -0700 Subject: [DAS2] how to test features? Message-ID: > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Andrew Dalke > Sent: Friday, June 10, 2005 10:14 AM > To: DAS/2 > Subject: Re: [DAS2] how to test features? > > Gregg: > > In DAS/1 the types response can optionally include a count of the > > number > > of features available for that particular type and source. I do think > > this would be a useful feature to preserve in DAS/2. > > I don't think it would work that well. Given the way we've > structured things it's possible the type/ hierarchy is shared > by several feature/ hierarchies. > > My two mental models are: > - a single server where different source/versions > shares the same types/ > - a server which uses someone else's types/ and regions/ > as the reference, adding only features/ I don't really see the problem with adding optional feature counts to the types response. I don't think that any established repository of genome annotations will be pointing to an external source for types, as you suggest above. That approach would affect not just feature counts but lots of other stuff in the types response, such as PROP elements and the soon-to-be added FORMAT elements. And without a _lot_ more information about what parameters were used when running the analysis, are you sure that your "BLAST" type is the same as some other site's "BLAST" type? Unless of course you copied the data from the other site in the first place, in which case we're talking about mirroring which to me is a different subject. To me the only potential problem is that without shared type ids we don't have a useful way of determining that two types from different servers (and possibly different genomes on the same server) are equivalent. But I'm far more comfortable with that situation than with the alternative, assuming that shared type ids really indicate the exact same analysis/annotation process. And we do have ways of determining that two types have some similarity -- that's what the ontology attribute is for. Furthermore, even if a DAS/2 server did refer to an external URI for a type id, it's not clear to me why that precludes it from adding a feature count attribute to the TYPE element that it returns from the types query. And the same applies to a server sharing the same types between sources and versions. Maybe this is semantics, but it seems to me that the types response is not meant to say "these are the types", but rather "these are the types and how they are used in the context of this versioned source". > > > From that > > information a client/validator could potentially tune its requested > > range to return on average a desired number of features. > > My shot-in-the-dark guess is that the non-uniform distribution > of features lessens its usefulness. Good point. > > I don't think a server should return only some of the features that > > meet > > the search criteria -- should return either all or none. If a server > > decides that a client is requesting too much data, I think servers > > should be able to return some sort of "returned feature count too > > large" > > error code response. > > I can go along with that, though I would like to know what > a client is supposed to do if it gets that response and > if we should specify that a server should be able to return at > least (say) 10,000 features at a time. > > > And maybe in the source or versioned source > > response xml have an optional indication of how many features a server > > is willing to serve up in a single request, so clients can know this > > limit in advance. > > In thinking some more about that - what would a client do > with that information? Well, since we've got alternative feature request formats, I've thought about a format that just returns a count of the features passing the filters. Which (assuming the server can respond to such a request quickly) would allow the client to "hunt around" till it found an appropriate range for the number of features the server maxes out at, or the number of features the client wants to restrict to. Another possibility if the client knows the upper limit of the server is a variant on what you suggested: > I was thinking that a "limit" option might be useful. > For example, "up to 1000 features in the range 1M to > 2M." 'Course then the server may need to report > "returned 1000 features but 234234 matched the query." But instead of limiting number of features returned within a range, have this be based on a single point, so it would be "get the 1000 features closest to this point". Not sure if this could be done as a "closest" filter (that just has a feature count) in combination with a region filter or if would need to have a combined filter that includes both a region and the count. If the latter then "get 1000 features nearest 500K on chr2" could just be something like: closest=chr2/500000:500000,1000 I know there was talk at one point about having a "get nearest neighbor" request in DAS/2. A "closest" filter would also address that functionality -- given that a feature location is seqA/pointB:pointC, then the filter for "get nearest neighbor of typeD" is: closest=seqA/pointB:pointC,1; type=typeD Would need to work out issues of what happens when there are multiple features with same location and "closest" filter only allows some of them through, or when there are multiple features that actually overlap the given point. gregg > > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From suzi at fruitfly.org Fri Jun 10 20:05:49 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Fri, 10 Jun 2005 13:05:49 -0700 Subject: [DAS2] specific aims Message-ID: As per our discussion yesterday, here they are. I'll be sending out the full outline anon (just have to adjust it to match the changes we made to the specific aims about). I'll try and tag names to sections that need to be written, but feel free to speak up if I've missed or gotten something wrong. -S -------------- next part -------------- A non-text attachment was scrubbed... Name: DAS2_specific_aims.doc Type: application/msword Size: 26624 bytes Desc: not available URL: From Gregg_Helt at affymetrix.com Fri Jun 10 20:27:08 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Fri, 10 Jun 2005 13:27:08 -0700 Subject: [DAS2] specific aims Message-ID: Adding a bit more info to what Suzi posted: We are applying for a continuation/renewal grant based on the current DAS/2 grant. The current grant expires in June 2006. This continuation would hopefully be for three years, starting in July 2006 and hopefully extending to July 2009. What Suzi posted is the start of a Specific Aims section for the grant. If you have any suggestions for what should be included (or excluded) in this grant, please post soon! The grant is due at NIH July 1, which means we really need the text finished by June 28th. Thanks, Gregg > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Suzanna Lewis > Sent: Friday, June 10, 2005 1:06 PM > To: das at biodas.org; > Cc: Mark Gibson; Nomi Harris; Sima Misra > Subject: [DAS2] specific aims > > As per our discussion yesterday, here they are. > > I'll be sending out the full outline anon (just have to > adjust it to match the changes we made to the > specific aims about). > > I'll try and tag names to sections that need to be > written, but feel free to speak up if I've missed or > gotten something wrong. > > -S > From allenday at ucla.edu Fri Jun 10 23:28:52 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 10 Jun 2005 16:28:52 -0700 (PDT) Subject: [DAS2] how to test features? In-Reply-To: References: Message-ID: Hi Gregg, I optimized the sql query, the transcript should now also take ~15s. -Allen On Fri, 10 Jun 2005, Helt,Gregg wrote: > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlap > s=chr21/22400000:22500000;type=SO:SNP > > and > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlap > s=chr21/22100000:22500000;type=SO:transcript > > Just tried them both again. The SNP request seemed to be noticeably > faster (returned in about 15 seconds) than the last time I tried it. > The transcript request seemed to still take a very long time (returned > in about 4 minutes). > > thanks, > gregg > > > > -----Original Message----- > > From: Allen Day [mailto:allenday at ucla.edu] > > Sent: Friday, June 10, 2005 12:31 PM > > To: Helt,Gregg > > Subject: RE: [DAS2] how to test features? > > > > Hi Gregg, > > > > Please send me your slow query URLs, I will use them as optimization > test > > cases. > > > > -Allen > From Gregg_Helt at affymetrix.com Thu Jun 16 15:35:27 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 16 Jun 2005 08:35:27 -0700 Subject: [DAS2] DAS/2 meeting pushed back to noon Pacific time Message-ID: By popular demand I'm shifting the regular weekly DAS/2 grant meeting today to noon Pacific time, to get around people's prior commitments. Unless anyone strongly objects, we'll make noon the set time from now on. Conference # 800-531-3250 (or 303-928-2693 if you're outside the US) Conference ID: 2879055 thanks, gregg From Gregg_Helt at affymetrix.com Thu Jun 16 17:06:52 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 16 Jun 2005 10:06:52 -0700 Subject: [DAS2] having problems with feature xml from test server Message-ID: I'm still having some problems on the client side with parsing DAS/2 feature xml from the biopackages server. Here's my test query: http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlap s=chr21/22100000:22500000;type=SO:mRNA The main problem I'm having is really due to ambiguity in the spec. In the feature xml response, the child features of an mRNA feature don't have a "parent" attribute giving the id of the parent feature. The mRNA feature does have sub-elements giving ids of its child features. But unless we specify that if there is a child/parent relationship both element in the parent and "parent" attribute in the child are required, there's no way of knowing until you've reached the end of the document whether a particular feature is a "root" feature, or whether it has a parent. And therefore you can't really implement a useful streaming parser. This came up before at the weekly meeting, but it hasn't been added to the spec change database yet - I'll add later today. thanks, gregg From Gregg_Helt at affymetrix.com Thu Jun 16 18:49:08 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 16 Jun 2005 11:49:08 -0700 Subject: [DAS2] Today's meeting agenda Message-ID: DAS/2 continuation grant Agenda for upcoming meetings at BOSC Spec Issues? Server implementation Client implementation Validation suite From Steve_Chervitz at affymetrix.com Thu Jun 16 20:44:24 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Thu, 16 Jun 2005 13:44:24 -0700 Subject: [DAS2] Re: DAS/2 meeting pushed back to noon Pacific time In-Reply-To: Message-ID: Ann's message was bounced by the DAS/2 list, not sure why, since she's on the list. Including it below. Steve --------------------------------------------------------------------------- From: Ann Loraine Date: Thu, 16 Jun 2005 13:25:20 -0500 To: "'Helt,Gregg '" , "'das2-bounces at portal.open-bio.org '" , 'DAS/2 ' Subject: RE: [DAS2] DAS/2 meeting pushed back to noon Pacific time Hi, I won't be attending due to a conflict with Arabidopsis meeting activities. See you at ISMB! btw, PlantGDB is planning to set up an Arabidopsis DAS by the end of the month. -Ann From boconnor at ucla.edu Mon Jun 20 18:04:48 2005 From: boconnor at ucla.edu (Brian O'Connor) Date: Mon, 20 Jun 2005 11:04:48 -0700 Subject: [DAS2] types and ontologies Message-ID: <42B70540.9070507@ucla.edu> Hi, I have a question about the status of this bug: http://bugzilla.open-bio.org/show_bug.cgi?id=1792. I'm working with Allen on an internal application that uses the /das/assay namespace to retrieve microarray data. What is the consensus on this bug? Are non-sequence features annotated with terms from other ontologies allowed? I know this is outside the scope of the current spec but I was curious what people think about this. Ideally I want to be able to query for which ontologies are available as well. For example something like: http://.../das/assay/chado/chado-Hsa-17/ontology/ would return an XML document describing the ontologies loaded. This could be used to filter a types query ie /das/assay/chado/chado-Hsa-17/type?namespace=foo.bar. Although I see Lincoln mentioned using a "brief" form on the type request to do essentially the same thing (bug http://bugzilla.open-bio.org/show_bug.cgi?id=1791). This seems like a reasonable way to go, how do other people feel? --Brian From Gregg_Helt at affymetrix.com Wed Jun 22 19:04:06 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Wed, 22 Jun 2005 12:04:06 -0700 Subject: [DAS2] Tentative DAS/2 meeting schedule Message-ID: Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me know what you think. gregg Thursday, June 23 1:30 PM - 3 PM Retrieval Spec 3:30 PM - 5 PM Registry and Discovery 5 PM - 6 PM Writeback Spec 6 PM - 7 PM Continuation Grant 7:00 PM Dinner Friday, June 24 1:30 PM - 4:30 PM Anything we didn't cover in first day? 5 PM -- ?? DAS/2 BOF From suzi at fruitfly.org Thu Jun 23 11:43:14 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Thu, 23 Jun 2005 07:43:14 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: References: Message-ID: <1c6f5047e8ebd3ff0ea08481b3ff1205@fruitfly.org> Where? On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me know > what > you think. > > gregg > > Thursday, June 23 > 1:30 PM - 3 PM Retrieval Spec > 3:30 PM - 5 PM Registry and Discovery > 5 PM - 6 PM Writeback Spec > 6 PM - 7 PM Continuation Grant > 7:00 PM Dinner > > Friday, June 24 > 1:30 PM - 4:30 PM Anything we didn't cover in first day? > 5 PM -- ?? DAS/2 BOF > > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From Gregg_Helt at affymetrix.com Thu Jun 23 15:19:19 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 23 Jun 2005 08:19:19 -0700 Subject: [DAS2] Tentative DAS/2 meeting schedule Message-ID: Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd floor) and figure it out from there. gregg > -----Original Message----- > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > Sent: Thursday, June 23, 2005 7:43 AM > To: Helt,Gregg > Cc: DAS/2 > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > Where? > > On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > > > Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me know > > what > > you think. > > > > gregg > > > > Thursday, June 23 > > 1:30 PM - 3 PM Retrieval Spec > > 3:30 PM - 5 PM Registry and Discovery > > 5 PM - 6 PM Writeback Spec > > 6 PM - 7 PM Continuation Grant > > 7:00 PM Dinner > > > > Friday, June 24 > > 1:30 PM - 4:30 PM Anything we didn't cover in first day? > > 5 PM -- ?? DAS/2 BOF > > > > > > _______________________________________________ > > DAS2 mailing list > > DAS2 at portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/das2 From suzi at fruitfly.org Thu Jun 23 15:29:58 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Thu, 23 Jun 2005 11:29:58 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: References: Message-ID: I may be a tad late since I have a conference call at noon. If I'm not there would someone give me a ring to let me know where to find you. (room 5219 or 510-909-7153) -S On Jun 23, 2005, at 11:19 AM, Helt,Gregg wrote: > Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd > floor) > and figure it out from there. > > gregg > >> -----Original Message----- >> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >> Sent: Thursday, June 23, 2005 7:43 AM >> To: Helt,Gregg >> Cc: DAS/2 >> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >> >> Where? >> >> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: >> >>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me know >>> what >>> you think. >>> >>> gregg >>> >>> Thursday, June 23 >>> 1:30 PM - 3 PM Retrieval Spec >>> 3:30 PM - 5 PM Registry and Discovery >>> 5 PM - 6 PM Writeback Spec >>> 6 PM - 7 PM Continuation Grant >>> 7:00 PM Dinner >>> >>> Friday, June 24 >>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? >>> 5 PM -- ?? DAS/2 BOF >>> >>> >>> _______________________________________________ >>> DAS2 mailing list >>> DAS2 at portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/das2 > From Gregg_Helt at affymetrix.com Thu Jun 23 15:30:10 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 23 Jun 2005 08:30:10 -0700 Subject: [DAS2] Notes from DAS/2 registry meeting, September 2004 Message-ID: I dug up my notes from the meeting about DAS/2 registry and discovery we had in Hinxton last September, should be attached as a doc file. A little spotty, but may be helpful for registry and discovery discussions later today. gregg -------------- next part -------------- A non-text attachment was scrubbed... Name: Das2RegistryNotes_Sep2004.doc Type: application/msword Size: 31744 bytes Desc: Das2RegistryNotes_Sep2004.doc URL: From Gregg_Helt at affymetrix.com Thu Jun 23 15:59:24 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 23 Jun 2005 08:59:24 -0700 Subject: [DAS2] More ideas for DAS/2 registry and discovery Message-ID: Here's another idea for a DAS/2 registry/discovery service that I've been thinking about for a while... -------------- next part -------------- A non-text attachment was scrubbed... Name: AnotherDas2RegistryIdea.doc Type: application/msword Size: 41984 bytes Desc: AnotherDas2RegistryIdea.doc URL: From Gregg_Helt at affymetrix.com Thu Jun 23 16:05:21 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 23 Jun 2005 09:05:21 -0700 Subject: [DAS2] Tentative DAS/2 meeting schedule Message-ID: Still trying to figure out DAS/2 meeting location today, hoping to start around 1:30 PM. Assuming we have access to a phone, for those of you who need to call in, here's the conference line info: Dial-in, domestic: 800-531-3250 International: 303-928-2693 Conference ID: 2879055 thanks, gregg > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Helt,Gregg > Sent: Thursday, June 23, 2005 11:19 AM > To: Suzanna Lewis > Cc: DAS/2 > Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > > Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd floor) > and figure it out from there. > > gregg > > > -----Original Message----- > > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > Sent: Thursday, June 23, 2005 7:43 AM > > To: Helt,Gregg > > Cc: DAS/2 > > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > > > Where? > > > > On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > > > > > Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me know > > > what > > > you think. > > > > > > gregg > > > > > > Thursday, June 23 > > > 1:30 PM - 3 PM Retrieval Spec > > > 3:30 PM - 5 PM Registry and Discovery > > > 5 PM - 6 PM Writeback Spec > > > 6 PM - 7 PM Continuation Grant > > > 7:00 PM Dinner > > > > > > Friday, June 24 > > > 1:30 PM - 4:30 PM Anything we didn't cover in first day? > > > 5 PM -- ?? DAS/2 BOF > > > > > > > > > _______________________________________________ > > > DAS2 mailing list > > > DAS2 at portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/das2 > > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From th at sanger.ac.uk Thu Jun 23 16:18:48 2005 From: th at sanger.ac.uk (Tim Hubbard) Date: Thu, 23 Jun 2005 17:18:48 +0100 Subject: [DAS2] Notes from DAS/2 registry meeting, September 2004 In-Reply-To: References: Message-ID: Hi Gregg, Hope you're all having fun out there. At 8:30 am -0700 23/6/05, Helt,Gregg wrote: >I dug up my notes from the meeting about DAS/2 registry and discovery we >had in Hinxton last September, should be attached as a doc file. A >little spotty, but may be helpful for registry and discovery discussions >later today. You might also want to take a look at the registry we've setup for DAS1 sources (=Andreas Prlic). http://das.sanger.ac.uk/registry/listServices.jsp So far the DAS sources that have been registered are mainly for proteins, however we are starting to register genomic sources and plan to use this for handling DAS sources within Ensembl shortly. This implementation has facilities built in to validate whether DAS sources are still available at regular intervals and flag ones that cannot be contacted and allows multiple registries through child/parent relationships Tim -- ------------------------------------------------------------------------- Dr Tim Hubbard email: th at sanger.ac.uk Wellcome Trust Sanger Institute Tel (direct): +44 1223 496886 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. URL: http://www.sanger.ac.uk/Users/th ------------------------------------------------------------------------- From suzi at fruitfly.org Thu Jun 23 17:45:35 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Thu, 23 Jun 2005 13:45:35 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: References: Message-ID: <4028d8d81683f8af8f71686d29e5854e@fruitfly.org> late breaking news. we're meeting at 2 in room c on the 39th flooor. On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > Still trying to figure out DAS/2 meeting location today, hoping to > start > around 1:30 PM. Assuming we have access to a phone, for those of you > who need to call in, here's the conference line info: > > Dial-in, domestic: 800-531-3250 > International: 303-928-2693 > Conference ID: 2879055 > > thanks, > gregg > >> -----Original Message----- >> From: das2-bounces at portal.open-bio.org > [mailto:das2-bounces at portal.open- >> bio.org] On Behalf Of Helt,Gregg >> Sent: Thursday, June 23, 2005 11:19 AM >> To: Suzanna Lewis >> Cc: DAS/2 >> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule >> >> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd > floor) >> and figure it out from there. >> >> gregg >> >>> -----Original Message----- >>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >>> Sent: Thursday, June 23, 2005 7:43 AM >>> To: Helt,Gregg >>> Cc: DAS/2 >>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>> >>> Where? >>> >>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: >>> >>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me > know >>>> what >>>> you think. >>>> >>>> gregg >>>> >>>> Thursday, June 23 >>>> 1:30 PM - 3 PM Retrieval Spec >>>> 3:30 PM - 5 PM Registry and Discovery >>>> 5 PM - 6 PM Writeback Spec >>>> 6 PM - 7 PM Continuation Grant >>>> 7:00 PM Dinner >>>> >>>> Friday, June 24 >>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? >>>> 5 PM -- ?? DAS/2 BOF >>>> >>>> >>>> _______________________________________________ >>>> DAS2 mailing list >>>> DAS2 at portal.open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/das2 >> >> >> _______________________________________________ >> DAS2 mailing list >> DAS2 at portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/das2 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From lstein at cshl.edu Fri Jun 24 15:14:23 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Fri, 24 Jun 2005 11:14:23 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: <4028d8d81683f8af8f71686d29e5854e@fruitfly.org> References: <4028d8d81683f8af8f71686d29e5854e@fruitfly.org> Message-ID: <200506241114.23974.lstein@cshl.edu> Hi, Are we still on for a DAS meeting (me by telephone) at 7 pm this evening? Lincoln On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: > late breaking news. > > we're meeting at 2 in room c on the 39th flooor. > > On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > > Still trying to figure out DAS/2 meeting location today, hoping to > > start > > around 1:30 PM. Assuming we have access to a phone, for those of you > > who need to call in, here's the conference line info: > > > > Dial-in, domestic: 800-531-3250 > > International: 303-928-2693 > > Conference ID: 2879055 > > > > thanks, > > gregg > > > >> -----Original Message----- > >> From: das2-bounces at portal.open-bio.org > > > > [mailto:das2-bounces at portal.open- > > > >> bio.org] On Behalf Of Helt,Gregg > >> Sent: Thursday, June 23, 2005 11:19 AM > >> To: Suzanna Lewis > >> Cc: DAS/2 > >> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > >> > >> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd > > > > floor) > > > >> and figure it out from there. > >> > >> gregg > >> > >>> -----Original Message----- > >>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] > >>> Sent: Thursday, June 23, 2005 7:43 AM > >>> To: Helt,Gregg > >>> Cc: DAS/2 > >>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > >>> > >>> Where? > >>> > >>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > >>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me > > > > know > > > >>>> what > >>>> you think. > >>>> > >>>> gregg > >>>> > >>>> Thursday, June 23 > >>>> 1:30 PM - 3 PM Retrieval Spec > >>>> 3:30 PM - 5 PM Registry and Discovery > >>>> 5 PM - 6 PM Writeback Spec > >>>> 6 PM - 7 PM Continuation Grant > >>>> 7:00 PM Dinner > >>>> > >>>> Friday, June 24 > >>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? > >>>> 5 PM -- ?? DAS/2 BOF > >>>> > >>>> > >>>> _______________________________________________ > >>>> DAS2 mailing list > >>>> DAS2 at portal.open-bio.org > >>>> http://portal.open-bio.org/mailman/listinfo/das2 > >> > >> _______________________________________________ > >> DAS2 mailing list > >> DAS2 at portal.open-bio.org > >> http://portal.open-bio.org/mailman/listinfo/das2 > > > > _______________________________________________ > > DAS2 mailing list > > DAS2 at portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/das2 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 -- Lincoln Stein lstein at cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From Gregg_Helt at affymetrix.com Fri Jun 24 20:45:04 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Fri, 24 Jun 2005 13:45:04 -0700 Subject: [DAS2] Tentative DAS/2 meeting schedule Message-ID: Yep, will that work for you? We're holding it in the Ambassador II room (where BOSC is), the hotel folks are supposed to install a speakerphone for us. Same teleconference numbers: Phone: 800-531-3250 Id: 2879055 thanks, gregg > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Lincoln Stein > Sent: Friday, June 24, 2005 11:14 AM > To: das2 at portal.open-bio.org > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > Hi, > > Are we still on for a DAS meeting (me by telephone) at 7 pm this evening? > > Lincoln > > On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: > > late breaking news. > > > > we're meeting at 2 in room c on the 39th flooor. > > > > On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > > > Still trying to figure out DAS/2 meeting location today, hoping to > > > start > > > around 1:30 PM. Assuming we have access to a phone, for those of you > > > who need to call in, here's the conference line info: > > > > > > Dial-in, domestic: 800-531-3250 > > > International: 303-928-2693 > > > Conference ID: 2879055 > > > > > > thanks, > > > gregg > > > > > >> -----Original Message----- > > >> From: das2-bounces at portal.open-bio.org > > > > > > [mailto:das2-bounces at portal.open- > > > > > >> bio.org] On Behalf Of Helt,Gregg > > >> Sent: Thursday, June 23, 2005 11:19 AM > > >> To: Suzanna Lewis > > >> Cc: DAS/2 > > >> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > > >> > > >> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd > > > > > > floor) > > > > > >> and figure it out from there. > > >> > > >> gregg > > >> > > >>> -----Original Message----- > > >>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > >>> Sent: Thursday, June 23, 2005 7:43 AM > > >>> To: Helt,Gregg > > >>> Cc: DAS/2 > > >>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >>> > > >>> Where? > > >>> > > >>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > > >>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me > > > > > > know > > > > > >>>> what > > >>>> you think. > > >>>> > > >>>> gregg > > >>>> > > >>>> Thursday, June 23 > > >>>> 1:30 PM - 3 PM Retrieval Spec > > >>>> 3:30 PM - 5 PM Registry and Discovery > > >>>> 5 PM - 6 PM Writeback Spec > > >>>> 6 PM - 7 PM Continuation Grant > > >>>> 7:00 PM Dinner > > >>>> > > >>>> Friday, June 24 > > >>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? > > >>>> 5 PM -- ?? DAS/2 BOF > > >>>> > > >>>> > > >>>> _______________________________________________ > > >>>> DAS2 mailing list > > >>>> DAS2 at portal.open-bio.org > > >>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >> > > >> _______________________________________________ > > >> DAS2 mailing list > > >> DAS2 at portal.open-bio.org > > >> http://portal.open-bio.org/mailman/listinfo/das2 > > > > > > _______________________________________________ > > > DAS2 mailing list > > > DAS2 at portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/das2 > > > > _______________________________________________ > > DAS2 mailing list > > DAS2 at portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/das2 > > -- > Lincoln Stein > lstein at cshl.edu > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From suzi at fruitfly.org Fri Jun 24 21:26:50 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Fri, 24 Jun 2005 17:26:50 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: References: Message-ID: <13255739cf06fa840d4145fc878b3410@fruitfly.org> I may be late, but I'll be there (Is anyone is bringing food?) On Jun 24, 2005, at 4:45 PM, Helt,Gregg wrote: > Yep, will that work for you? We're holding it in the Ambassador II > room > (where BOSC is), the hotel folks are supposed to install a speakerphone > for us. Same teleconference numbers: > Phone: 800-531-3250 > Id: 2879055 > > thanks, > gregg > >> -----Original Message----- >> From: das2-bounces at portal.open-bio.org > [mailto:das2-bounces at portal.open- >> bio.org] On Behalf Of Lincoln Stein >> Sent: Friday, June 24, 2005 11:14 AM >> To: das2 at portal.open-bio.org >> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >> >> Hi, >> >> Are we still on for a DAS meeting (me by telephone) at 7 pm this > evening? >> >> Lincoln >> >> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: >>> late breaking news. >>> >>> we're meeting at 2 in room c on the 39th flooor. >>> >>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: >>>> Still trying to figure out DAS/2 meeting location today, hoping to >>>> start >>>> around 1:30 PM. Assuming we have access to a phone, for those of > you >>>> who need to call in, here's the conference line info: >>>> >>>> Dial-in, domestic: 800-531-3250 >>>> International: 303-928-2693 >>>> Conference ID: 2879055 >>>> >>>> thanks, >>>> gregg >>>> >>>>> -----Original Message----- >>>>> From: das2-bounces at portal.open-bio.org >>>> >>>> [mailto:das2-bounces at portal.open- >>>> >>>>> bio.org] On Behalf Of Helt,Gregg >>>>> Sent: Thursday, June 23, 2005 11:19 AM >>>>> To: Suzanna Lewis >>>>> Cc: DAS/2 >>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule >>>>> >>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd >>>> >>>> floor) >>>> >>>>> and figure it out from there. >>>>> >>>>> gregg >>>>> >>>>>> -----Original Message----- >>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >>>>>> Sent: Thursday, June 23, 2005 7:43 AM >>>>>> To: Helt,Gregg >>>>>> Cc: DAS/2 >>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>> >>>>>> Where? >>>>>> >>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: >>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me >>>> >>>> know >>>> >>>>>>> what >>>>>>> you think. >>>>>>> >>>>>>> gregg >>>>>>> >>>>>>> Thursday, June 23 >>>>>>> 1:30 PM - 3 PM Retrieval Spec >>>>>>> 3:30 PM - 5 PM Registry and Discovery >>>>>>> 5 PM - 6 PM Writeback Spec >>>>>>> 6 PM - 7 PM Continuation Grant >>>>>>> 7:00 PM Dinner >>>>>>> >>>>>>> Friday, June 24 >>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? >>>>>>> 5 PM -- ?? DAS/2 BOF >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> DAS2 mailing list >>>>>>> DAS2 at portal.open-bio.org >>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>> >>>>> _______________________________________________ >>>>> DAS2 mailing list >>>>> DAS2 at portal.open-bio.org >>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>> >>>> _______________________________________________ >>>> DAS2 mailing list >>>> DAS2 at portal.open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/das2 >>> >>> _______________________________________________ >>> DAS2 mailing list >>> DAS2 at portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/das2 >> >> -- >> Lincoln Stein >> lstein at cshl.edu >> Cold Spring Harbor Laboratory >> 1 Bungtown Road >> Cold Spring Harbor, NY 11724 >> (516) 367-8380 (voice) >> (516) 367-8389 (fax) >> _______________________________________________ >> DAS2 mailing list >> DAS2 at portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/das2 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From lstein at cshl.edu Fri Jun 24 18:18:10 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Fri, 24 Jun 2005 14:18:10 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: References: Message-ID: <200506241418.10570.lstein@cshl.edu> Sounds good! Lincoln On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: > Yep, will that work for you? We're holding it in the Ambassador II room > (where BOSC is), the hotel folks are supposed to install a speakerphone > for us. Same teleconference numbers: > Phone: 800-531-3250 > Id: 2879055 > > thanks, > gregg > > > -----Original Message----- > > From: das2-bounces at portal.open-bio.org > > [mailto:das2-bounces at portal.open- > > > bio.org] On Behalf Of Lincoln Stein > > Sent: Friday, June 24, 2005 11:14 AM > > To: das2 at portal.open-bio.org > > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > > > Hi, > > > > Are we still on for a DAS meeting (me by telephone) at 7 pm this > > evening? > > > Lincoln > > > > On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: > > > late breaking news. > > > > > > we're meeting at 2 in room c on the 39th flooor. > > > > > > On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > > > > Still trying to figure out DAS/2 meeting location today, hoping to > > > > start > > > > around 1:30 PM. Assuming we have access to a phone, for those of > > you > > > > > who need to call in, here's the conference line info: > > > > > > > > Dial-in, domestic: 800-531-3250 > > > > International: 303-928-2693 > > > > Conference ID: 2879055 > > > > > > > > thanks, > > > > gregg > > > > > > > >> -----Original Message----- > > > >> From: das2-bounces at portal.open-bio.org > > > > > > > > [mailto:das2-bounces at portal.open- > > > > > > > >> bio.org] On Behalf Of Helt,Gregg > > > >> Sent: Thursday, June 23, 2005 11:19 AM > > > >> To: Suzanna Lewis > > > >> Cc: DAS/2 > > > >> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > > > >> > > > >> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd > > > > > > > > floor) > > > > > > > >> and figure it out from there. > > > >> > > > >> gregg > > > >> > > > >>> -----Original Message----- > > > >>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > > >>> Sent: Thursday, June 23, 2005 7:43 AM > > > >>> To: Helt,Gregg > > > >>> Cc: DAS/2 > > > >>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > > >>> > > > >>> Where? > > > >>> > > > >>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > > > >>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me > > > > > > > > know > > > > > > > >>>> what > > > >>>> you think. > > > >>>> > > > >>>> gregg > > > >>>> > > > >>>> Thursday, June 23 > > > >>>> 1:30 PM - 3 PM Retrieval Spec > > > >>>> 3:30 PM - 5 PM Registry and Discovery > > > >>>> 5 PM - 6 PM Writeback Spec > > > >>>> 6 PM - 7 PM Continuation Grant > > > >>>> 7:00 PM Dinner > > > >>>> > > > >>>> Friday, June 24 > > > >>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? > > > >>>> 5 PM -- ?? DAS/2 BOF > > > >>>> > > > >>>> > > > >>>> _______________________________________________ > > > >>>> DAS2 mailing list > > > >>>> DAS2 at portal.open-bio.org > > > >>>> http://portal.open-bio.org/mailman/listinfo/das2 > > > >> > > > >> _______________________________________________ > > > >> DAS2 mailing list > > > >> DAS2 at portal.open-bio.org > > > >> http://portal.open-bio.org/mailman/listinfo/das2 > > > > > > > > _______________________________________________ > > > > DAS2 mailing list > > > > DAS2 at portal.open-bio.org > > > > http://portal.open-bio.org/mailman/listinfo/das2 > > > > > > _______________________________________________ > > > DAS2 mailing list > > > DAS2 at portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/das2 > > > > -- > > Lincoln Stein > > lstein at cshl.edu > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > _______________________________________________ > > DAS2 mailing list > > DAS2 at portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/das2 -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From Gregg_Helt at affymetrix.com Fri Jun 24 23:08:33 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Fri, 24 Jun 2005 16:08:33 -0700 Subject: [DAS2] Tentative DAS/2 meeting schedule Message-ID: Apologies, looks like we lost the room I was planning to meet in (and the speakerphone). I think we better reschedule. How about starting up again on Sunday? Gregg > -----Original Message----- > From: Lincoln Stein [mailto:lstein at cshl.edu] > Sent: Friday, June 24, 2005 2:18 PM > To: Helt,Gregg > Cc: das2 at portal.open-bio.org > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > Sounds good! > > Lincoln > > On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: > > Yep, will that work for you? We're holding it in the Ambassador II room > > (where BOSC is), the hotel folks are supposed to install a speakerphone > > for us. Same teleconference numbers: > > Phone: 800-531-3250 > > Id: 2879055 > > > > thanks, > > gregg > > > > > -----Original Message----- > > > From: das2-bounces at portal.open-bio.org > > > > [mailto:das2-bounces at portal.open- > > > > > bio.org] On Behalf Of Lincoln Stein > > > Sent: Friday, June 24, 2005 11:14 AM > > > To: das2 at portal.open-bio.org > > > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > > > > > Hi, > > > > > > Are we still on for a DAS meeting (me by telephone) at 7 pm this > > > > evening? > > > > > Lincoln > > > > > > On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: > > > > late breaking news. > > > > > > > > we're meeting at 2 in room c on the 39th flooor. > > > > > > > > On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > > > > > Still trying to figure out DAS/2 meeting location today, hoping to > > > > > start > > > > > around 1:30 PM. Assuming we have access to a phone, for those of > > > > you > > > > > > > who need to call in, here's the conference line info: > > > > > > > > > > Dial-in, domestic: 800-531-3250 > > > > > International: 303-928-2693 > > > > > Conference ID: 2879055 > > > > > > > > > > thanks, > > > > > gregg > > > > > > > > > >> -----Original Message----- > > > > >> From: das2-bounces at portal.open-bio.org > > > > > > > > > > [mailto:das2-bounces at portal.open- > > > > > > > > > >> bio.org] On Behalf Of Helt,Gregg > > > > >> Sent: Thursday, June 23, 2005 11:19 AM > > > > >> To: Suzanna Lewis > > > > >> Cc: DAS/2 > > > > >> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > > > > >> > > > > >> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby (3rd > > > > > > > > > > floor) > > > > > > > > > >> and figure it out from there. > > > > >> > > > > >> gregg > > > > >> > > > > >>> -----Original Message----- > > > > >>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > > > >>> Sent: Thursday, June 23, 2005 7:43 AM > > > > >>> To: Helt,Gregg > > > > >>> Cc: DAS/2 > > > > >>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > > > >>> > > > > >>> Where? > > > > >>> > > > > >>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > > > > >>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let me > > > > > > > > > > know > > > > > > > > > >>>> what > > > > >>>> you think. > > > > >>>> > > > > >>>> gregg > > > > >>>> > > > > >>>> Thursday, June 23 > > > > >>>> 1:30 PM - 3 PM Retrieval Spec > > > > >>>> 3:30 PM - 5 PM Registry and Discovery > > > > >>>> 5 PM - 6 PM Writeback Spec > > > > >>>> 6 PM - 7 PM Continuation Grant > > > > >>>> 7:00 PM Dinner > > > > >>>> > > > > >>>> Friday, June 24 > > > > >>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? > > > > >>>> 5 PM -- ?? DAS/2 BOF > > > > >>>> > > > > >>>> > > > > >>>> _______________________________________________ > > > > >>>> DAS2 mailing list > > > > >>>> DAS2 at portal.open-bio.org > > > > >>>> http://portal.open-bio.org/mailman/listinfo/das2 > > > > >> > > > > >> _______________________________________________ > > > > >> DAS2 mailing list > > > > >> DAS2 at portal.open-bio.org > > > > >> http://portal.open-bio.org/mailman/listinfo/das2 > > > > > > > > > > _______________________________________________ > > > > > DAS2 mailing list > > > > > DAS2 at portal.open-bio.org > > > > > http://portal.open-bio.org/mailman/listinfo/das2 > > > > > > > > _______________________________________________ > > > > DAS2 mailing list > > > > DAS2 at portal.open-bio.org > > > > http://portal.open-bio.org/mailman/listinfo/das2 > > > > > > -- > > > Lincoln Stein > > > lstein at cshl.edu > > > Cold Spring Harbor Laboratory > > > 1 Bungtown Road > > > Cold Spring Harbor, NY 11724 > > > (516) 367-8380 (voice) > > > (516) 367-8389 (fax) > > > _______________________________________________ > > > DAS2 mailing list > > > DAS2 at portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/das2 > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 From suzi at fruitfly.org Fri Jun 24 23:56:23 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Fri, 24 Jun 2005 19:56:23 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: References: Message-ID: <8a4e2260f0f734d92b43b789f93dc940@fruitfly.org> Ah, I was wondering why I didn't find you there. Sunday morn would work for me. On Jun 24, 2005, at 7:08 PM, Helt,Gregg wrote: > Apologies, looks like we lost the room I was planning to meet in (and > the speakerphone). I think we better reschedule. How about starting > up > again on Sunday? > > Gregg > > >> -----Original Message----- >> From: Lincoln Stein [mailto:lstein at cshl.edu] >> Sent: Friday, June 24, 2005 2:18 PM >> To: Helt,Gregg >> Cc: das2 at portal.open-bio.org >> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >> >> Sounds good! >> >> Lincoln >> >> On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: >>> Yep, will that work for you? We're holding it in the Ambassador II > room >>> (where BOSC is), the hotel folks are supposed to install a > speakerphone >>> for us. Same teleconference numbers: >>> Phone: 800-531-3250 >>> Id: 2879055 >>> >>> thanks, >>> gregg >>> >>>> -----Original Message----- >>>> From: das2-bounces at portal.open-bio.org >>> >>> [mailto:das2-bounces at portal.open- >>> >>>> bio.org] On Behalf Of Lincoln Stein >>>> Sent: Friday, June 24, 2005 11:14 AM >>>> To: das2 at portal.open-bio.org >>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>> >>>> Hi, >>>> >>>> Are we still on for a DAS meeting (me by telephone) at 7 pm this >>> >>> evening? >>> >>>> Lincoln >>>> >>>> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: >>>>> late breaking news. >>>>> >>>>> we're meeting at 2 in room c on the 39th flooor. >>>>> >>>>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: >>>>>> Still trying to figure out DAS/2 meeting location today, > hoping to >>>>>> start >>>>>> around 1:30 PM. Assuming we have access to a phone, for those > of >>> >>> you >>> >>>>>> who need to call in, here's the conference line info: >>>>>> >>>>>> Dial-in, domestic: 800-531-3250 >>>>>> International: 303-928-2693 >>>>>> Conference ID: 2879055 >>>>>> >>>>>> thanks, >>>>>> gregg >>>>>> >>>>>>> -----Original Message----- >>>>>>> From: das2-bounces at portal.open-bio.org >>>>>> >>>>>> [mailto:das2-bounces at portal.open- >>>>>> >>>>>>> bio.org] On Behalf Of Helt,Gregg >>>>>>> Sent: Thursday, June 23, 2005 11:19 AM >>>>>>> To: Suzanna Lewis >>>>>>> Cc: DAS/2 >>>>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule >>>>>>> >>>>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby > (3rd >>>>>> >>>>>> floor) >>>>>> >>>>>>> and figure it out from there. >>>>>>> >>>>>>> gregg >>>>>>> >>>>>>>> -----Original Message----- >>>>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >>>>>>>> Sent: Thursday, June 23, 2005 7:43 AM >>>>>>>> To: Helt,Gregg >>>>>>>> Cc: DAS/2 >>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>> >>>>>>>> Where? >>>>>>>> >>>>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: >>>>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let > me >>>>>> >>>>>> know >>>>>> >>>>>>>>> what >>>>>>>>> you think. >>>>>>>>> >>>>>>>>> gregg >>>>>>>>> >>>>>>>>> Thursday, June 23 >>>>>>>>> 1:30 PM - 3 PM Retrieval Spec >>>>>>>>> 3:30 PM - 5 PM Registry and Discovery >>>>>>>>> 5 PM - 6 PM Writeback Spec >>>>>>>>> 6 PM - 7 PM Continuation Grant >>>>>>>>> 7:00 PM Dinner >>>>>>>>> >>>>>>>>> Friday, June 24 >>>>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? >>>>>>>>> 5 PM -- ?? DAS/2 BOF >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> DAS2 mailing list >>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>> >>>>>>> _______________________________________________ >>>>>>> DAS2 mailing list >>>>>>> DAS2 at portal.open-bio.org >>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>> >>>>>> _______________________________________________ >>>>>> DAS2 mailing list >>>>>> DAS2 at portal.open-bio.org >>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>> >>>>> _______________________________________________ >>>>> DAS2 mailing list >>>>> DAS2 at portal.open-bio.org >>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>> >>>> -- >>>> Lincoln Stein >>>> lstein at cshl.edu >>>> Cold Spring Harbor Laboratory >>>> 1 Bungtown Road >>>> Cold Spring Harbor, NY 11724 >>>> (516) 367-8380 (voice) >>>> (516) 367-8389 (fax) >>>> _______________________________________________ >>>> DAS2 mailing list >>>> DAS2 at portal.open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/das2 >> >> -- >> Lincoln D. Stein >> Cold Spring Harbor Laboratory >> 1 Bungtown Road >> Cold Spring Harbor, NY 11724 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From suzi at fruitfly.org Sun Jun 26 01:30:51 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Sat, 25 Jun 2005 21:30:51 -0400 Subject: [DAS2] Monday for next meeting Message-ID: <56b5ba368d05b3346567807d1a1bdedd@fruitfly.org> Hi all, just received a voice message from Gregg. He can't arrange a meeting room for Sunday, but will/can do this for Monday (27th). Details to follow. This is just to let you know that Sunday is a day off (as far as DAS work). best, S From Steve_Chervitz at affymetrix.com Sun Jun 26 15:26:23 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Sun, 26 Jun 2005 08:26:23 -0700 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: <8a4e2260f0f734d92b43b789f93dc940@fruitfly.org> Message-ID: Is there a meeting on for today? Did it happen already? Gregg: Are you going to be back at ISMB today? Steve > From: Suzanna Lewis > Date: Fri, 24 Jun 2005 19:56:23 -0400 > To: "Helt,Gregg" > Cc: > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > Ah, I was wondering why I didn't find you there. Sunday morn would work > for me. > > On Jun 24, 2005, at 7:08 PM, Helt,Gregg wrote: > >> Apologies, looks like we lost the room I was planning to meet in (and >> the speakerphone). I think we better reschedule. How about starting >> up >> again on Sunday? >> >> Gregg >> >> >>> -----Original Message----- >>> From: Lincoln Stein [mailto:lstein at cshl.edu] >>> Sent: Friday, June 24, 2005 2:18 PM >>> To: Helt,Gregg >>> Cc: das2 at portal.open-bio.org >>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>> >>> Sounds good! >>> >>> Lincoln >>> >>> On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: >>>> Yep, will that work for you? We're holding it in the Ambassador II >> room >>>> (where BOSC is), the hotel folks are supposed to install a >> speakerphone >>>> for us. Same teleconference numbers: >>>> Phone: 800-531-3250 >>>> Id: 2879055 >>>> >>>> thanks, >>>> gregg >>>> >>>>> -----Original Message----- >>>>> From: das2-bounces at portal.open-bio.org >>>> >>>> [mailto:das2-bounces at portal.open- >>>> >>>>> bio.org] On Behalf Of Lincoln Stein >>>>> Sent: Friday, June 24, 2005 11:14 AM >>>>> To: das2 at portal.open-bio.org >>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>> >>>>> Hi, >>>>> >>>>> Are we still on for a DAS meeting (me by telephone) at 7 pm this >>>> >>>> evening? >>>> >>>>> Lincoln >>>>> >>>>> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: >>>>>> late breaking news. >>>>>> >>>>>> we're meeting at 2 in room c on the 39th flooor. >>>>>> >>>>>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: >>>>>>> Still trying to figure out DAS/2 meeting location today, >> hoping to >>>>>>> start >>>>>>> around 1:30 PM. Assuming we have access to a phone, for those >> of >>>> >>>> you >>>> >>>>>>> who need to call in, here's the conference line info: >>>>>>> >>>>>>> Dial-in, domestic: 800-531-3250 >>>>>>> International: 303-928-2693 >>>>>>> Conference ID: 2879055 >>>>>>> >>>>>>> thanks, >>>>>>> gregg >>>>>>> >>>>>>>> -----Original Message----- >>>>>>>> From: das2-bounces at portal.open-bio.org >>>>>>> >>>>>>> [mailto:das2-bounces at portal.open- >>>>>>> >>>>>>>> bio.org] On Behalf Of Helt,Gregg >>>>>>>> Sent: Thursday, June 23, 2005 11:19 AM >>>>>>>> To: Suzanna Lewis >>>>>>>> Cc: DAS/2 >>>>>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>> >>>>>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby >> (3rd >>>>>>> >>>>>>> floor) >>>>>>> >>>>>>>> and figure it out from there. >>>>>>>> >>>>>>>> gregg >>>>>>>> >>>>>>>>> -----Original Message----- >>>>>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >>>>>>>>> Sent: Thursday, June 23, 2005 7:43 AM >>>>>>>>> To: Helt,Gregg >>>>>>>>> Cc: DAS/2 >>>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>>> >>>>>>>>> Where? >>>>>>>>> >>>>>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: >>>>>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let >> me >>>>>>> >>>>>>> know >>>>>>> >>>>>>>>>> what >>>>>>>>>> you think. >>>>>>>>>> >>>>>>>>>> gregg >>>>>>>>>> >>>>>>>>>> Thursday, June 23 >>>>>>>>>> 1:30 PM - 3 PM Retrieval Spec >>>>>>>>>> 3:30 PM - 5 PM Registry and Discovery >>>>>>>>>> 5 PM - 6 PM Writeback Spec >>>>>>>>>> 6 PM - 7 PM Continuation Grant >>>>>>>>>> 7:00 PM Dinner >>>>>>>>>> >>>>>>>>>> Friday, June 24 >>>>>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? >>>>>>>>>> 5 PM -- ?? DAS/2 BOF >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> DAS2 mailing list >>>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> DAS2 mailing list >>>>>>>> DAS2 at portal.open-bio.org >>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>> >>>>>>> _______________________________________________ >>>>>>> DAS2 mailing list >>>>>>> DAS2 at portal.open-bio.org >>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>> >>>>>> _______________________________________________ >>>>>> DAS2 mailing list >>>>>> DAS2 at portal.open-bio.org >>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>> >>>>> -- >>>>> Lincoln Stein >>>>> lstein at cshl.edu >>>>> Cold Spring Harbor Laboratory >>>>> 1 Bungtown Road >>>>> Cold Spring Harbor, NY 11724 >>>>> (516) 367-8380 (voice) >>>>> (516) 367-8389 (fax) >>>>> _______________________________________________ >>>>> DAS2 mailing list >>>>> DAS2 at portal.open-bio.org >>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>> >>> -- >>> Lincoln D. Stein >>> Cold Spring Harbor Laboratory >>> 1 Bungtown Road >>> Cold Spring Harbor, NY 11724 >> >> _______________________________________________ >> DAS2 mailing list >> DAS2 at portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/das2 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From suzi at fruitfly.org Sun Jun 26 15:29:26 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Sun, 26 Jun 2005 11:29:26 -0400 Subject: [DAS2] Tentative DAS/2 meeting schedule In-Reply-To: References: Message-ID: <9247240106245d1ec052ca92d38d3c02@fruitfly.org> No meeting today. Gregg will be back latter today to arrange a room for tomorrow and let us know. (appears like my last mail didn't get through) On Jun 26, 2005, at 11:26 AM, Chervitz, Steve wrote: > Is there a meeting on for today? Did it happen already? Gregg: Are you > going > to be back at ISMB today? > > Steve > > >> From: Suzanna Lewis >> Date: Fri, 24 Jun 2005 19:56:23 -0400 >> To: "Helt,Gregg" >> Cc: >> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >> >> Ah, I was wondering why I didn't find you there. Sunday morn would >> work >> for me. >> >> On Jun 24, 2005, at 7:08 PM, Helt,Gregg wrote: >> >>> Apologies, looks like we lost the room I was planning to meet in (and >>> the speakerphone). I think we better reschedule. How about starting >>> up >>> again on Sunday? >>> >>> Gregg >>> >>> >>>> -----Original Message----- >>>> From: Lincoln Stein [mailto:lstein at cshl.edu] >>>> Sent: Friday, June 24, 2005 2:18 PM >>>> To: Helt,Gregg >>>> Cc: das2 at portal.open-bio.org >>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>> >>>> Sounds good! >>>> >>>> Lincoln >>>> >>>> On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: >>>>> Yep, will that work for you? We're holding it in the Ambassador II >>> room >>>>> (where BOSC is), the hotel folks are supposed to install a >>> speakerphone >>>>> for us. Same teleconference numbers: >>>>> Phone: 800-531-3250 >>>>> Id: 2879055 >>>>> >>>>> thanks, >>>>> gregg >>>>> >>>>>> -----Original Message----- >>>>>> From: das2-bounces at portal.open-bio.org >>>>> >>>>> [mailto:das2-bounces at portal.open- >>>>> >>>>>> bio.org] On Behalf Of Lincoln Stein >>>>>> Sent: Friday, June 24, 2005 11:14 AM >>>>>> To: das2 at portal.open-bio.org >>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>> >>>>>> Hi, >>>>>> >>>>>> Are we still on for a DAS meeting (me by telephone) at 7 pm this >>>>> >>>>> evening? >>>>> >>>>>> Lincoln >>>>>> >>>>>> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: >>>>>>> late breaking news. >>>>>>> >>>>>>> we're meeting at 2 in room c on the 39th flooor. >>>>>>> >>>>>>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: >>>>>>>> Still trying to figure out DAS/2 meeting location today, >>> hoping to >>>>>>>> start >>>>>>>> around 1:30 PM. Assuming we have access to a phone, for those >>> of >>>>> >>>>> you >>>>> >>>>>>>> who need to call in, here's the conference line info: >>>>>>>> >>>>>>>> Dial-in, domestic: 800-531-3250 >>>>>>>> International: 303-928-2693 >>>>>>>> Conference ID: 2879055 >>>>>>>> >>>>>>>> thanks, >>>>>>>> gregg >>>>>>>> >>>>>>>>> -----Original Message----- >>>>>>>>> From: das2-bounces at portal.open-bio.org >>>>>>>> >>>>>>>> [mailto:das2-bounces at portal.open- >>>>>>>> >>>>>>>>> bio.org] On Behalf Of Helt,Gregg >>>>>>>>> Sent: Thursday, June 23, 2005 11:19 AM >>>>>>>>> To: Suzanna Lewis >>>>>>>>> Cc: DAS/2 >>>>>>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>>> >>>>>>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby >>> (3rd >>>>>>>> >>>>>>>> floor) >>>>>>>> >>>>>>>>> and figure it out from there. >>>>>>>>> >>>>>>>>> gregg >>>>>>>>> >>>>>>>>>> -----Original Message----- >>>>>>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >>>>>>>>>> Sent: Thursday, June 23, 2005 7:43 AM >>>>>>>>>> To: Helt,Gregg >>>>>>>>>> Cc: DAS/2 >>>>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>>>> >>>>>>>>>> Where? >>>>>>>>>> >>>>>>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: >>>>>>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let >>> me >>>>>>>> >>>>>>>> know >>>>>>>> >>>>>>>>>>> what >>>>>>>>>>> you think. >>>>>>>>>>> >>>>>>>>>>> gregg >>>>>>>>>>> >>>>>>>>>>> Thursday, June 23 >>>>>>>>>>> 1:30 PM - 3 PM Retrieval Spec >>>>>>>>>>> 3:30 PM - 5 PM Registry and Discovery >>>>>>>>>>> 5 PM - 6 PM Writeback Spec >>>>>>>>>>> 6 PM - 7 PM Continuation Grant >>>>>>>>>>> 7:00 PM Dinner >>>>>>>>>>> >>>>>>>>>>> Friday, June 24 >>>>>>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? >>>>>>>>>>> 5 PM -- ?? DAS/2 BOF >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> DAS2 mailing list >>>>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> DAS2 mailing list >>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> DAS2 mailing list >>>>>>>> DAS2 at portal.open-bio.org >>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>> >>>>>>> _______________________________________________ >>>>>>> DAS2 mailing list >>>>>>> DAS2 at portal.open-bio.org >>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>> >>>>>> -- >>>>>> Lincoln Stein >>>>>> lstein at cshl.edu >>>>>> Cold Spring Harbor Laboratory >>>>>> 1 Bungtown Road >>>>>> Cold Spring Harbor, NY 11724 >>>>>> (516) 367-8380 (voice) >>>>>> (516) 367-8389 (fax) >>>>>> _______________________________________________ >>>>>> DAS2 mailing list >>>>>> DAS2 at portal.open-bio.org >>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>> >>>> -- >>>> Lincoln D. Stein >>>> Cold Spring Harbor Laboratory >>>> 1 Bungtown Road >>>> Cold Spring Harbor, NY 11724 >>> >>> _______________________________________________ >>> DAS2 mailing list >>> DAS2 at portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/das2 >> >> _______________________________________________ >> DAS2 mailing list >> DAS2 at portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/das2 > From lstein at cshl.edu Sun Jun 26 17:08:35 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Sun, 26 Jun 2005 13:08:35 -0400 Subject: [DAS2] Monday for next meeting In-Reply-To: <56b5ba368d05b3346567807d1a1bdedd@fruitfly.org> References: <56b5ba368d05b3346567807d1a1bdedd@fruitfly.org> Message-ID: <200506261308.36358.lstein@cshl.edu> Hi Suzi, I'm not shedding any tears over this! Lincoln On Saturday 25 June 2005 09:30 pm, Suzanna Lewis wrote: > Hi all, > > just received a voice message from Gregg. He can't arrange a meeting > room for Sunday, but will/can do this for Monday (27th). Details to > follow. This is just to let you know that Sunday is a day off (as far > as DAS work). > > best, S > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From Gregg_Helt at affymetrix.com Sun Jun 26 22:35:19 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Sun, 26 Jun 2005 15:35:19 -0700 Subject: [DAS2] DAS/2 meeting schedule for Monday Message-ID: I've reserved a room for a DAS/2 meeting tomorrow (Monday), Duluth (on the 5th floor), from 2PM to 6PM Eastern time. It also comes with a better speakerphone than what we had last time. Lincoln and Allen, please let me know as soon as possible if you can't make it! With a four hour window, I'm hoping you can both teleconference in for at least part of the meeting. I've also tentatively reserved the same room for 2PM to 5 PM Tuesday, Eastern time. Conference phone #: 800-531-3250 Conference id: 2879055 gregg > -----Original Message----- > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > Sent: Sunday, June 26, 2005 11:29 AM > To: Chervitz, Steve > Cc: Helt,Gregg; das2 at portal.open-bio.org > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > No meeting today. Gregg will be back latter today to arrange a room for > tomorrow and let us know. (appears like my last mail didn't get > through) > > > On Jun 26, 2005, at 11:26 AM, Chervitz, Steve wrote: > > > Is there a meeting on for today? Did it happen already? Gregg: Are you > > going > > to be back at ISMB today? > > > > Steve > > > > > >> From: Suzanna Lewis > >> Date: Fri, 24 Jun 2005 19:56:23 -0400 > >> To: "Helt,Gregg" > >> Cc: > >> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > >> > >> Ah, I was wondering why I didn't find you there. Sunday morn would > >> work > >> for me. > >> > >> On Jun 24, 2005, at 7:08 PM, Helt,Gregg wrote: > >> > >>> Apologies, looks like we lost the room I was planning to meet in (and > >>> the speakerphone). I think we better reschedule. How about starting > >>> up > >>> again on Sunday? > >>> > >>> Gregg > >>> > >>> > >>>> -----Original Message----- > >>>> From: Lincoln Stein [mailto:lstein at cshl.edu] > >>>> Sent: Friday, June 24, 2005 2:18 PM > >>>> To: Helt,Gregg > >>>> Cc: das2 at portal.open-bio.org > >>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > >>>> > >>>> Sounds good! > >>>> > >>>> Lincoln > >>>> > >>>> On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: > >>>>> Yep, will that work for you? We're holding it in the Ambassador II > >>> room > >>>>> (where BOSC is), the hotel folks are supposed to install a > >>> speakerphone > >>>>> for us. Same teleconference numbers: > >>>>> Phone: 800-531-3250 > >>>>> Id: 2879055 > >>>>> > >>>>> thanks, > >>>>> gregg > >>>>> > >>>>>> -----Original Message----- > >>>>>> From: das2-bounces at portal.open-bio.org > >>>>> > >>>>> [mailto:das2-bounces at portal.open- > >>>>> > >>>>>> bio.org] On Behalf Of Lincoln Stein > >>>>>> Sent: Friday, June 24, 2005 11:14 AM > >>>>>> To: das2 at portal.open-bio.org > >>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > >>>>>> > >>>>>> Hi, > >>>>>> > >>>>>> Are we still on for a DAS meeting (me by telephone) at 7 pm this > >>>>> > >>>>> evening? > >>>>> > >>>>>> Lincoln > >>>>>> > >>>>>> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: > >>>>>>> late breaking news. > >>>>>>> > >>>>>>> we're meeting at 2 in room c on the 39th flooor. > >>>>>>> > >>>>>>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > >>>>>>>> Still trying to figure out DAS/2 meeting location today, > >>> hoping to > >>>>>>>> start > >>>>>>>> around 1:30 PM. Assuming we have access to a phone, for those > >>> of > >>>>> > >>>>> you > >>>>> > >>>>>>>> who need to call in, here's the conference line info: > >>>>>>>> > >>>>>>>> Dial-in, domestic: 800-531-3250 > >>>>>>>> International: 303-928-2693 > >>>>>>>> Conference ID: 2879055 > >>>>>>>> > >>>>>>>> thanks, > >>>>>>>> gregg > >>>>>>>> > >>>>>>>>> -----Original Message----- > >>>>>>>>> From: das2-bounces at portal.open-bio.org > >>>>>>>> > >>>>>>>> [mailto:das2-bounces at portal.open- > >>>>>>>> > >>>>>>>>> bio.org] On Behalf Of Helt,Gregg > >>>>>>>>> Sent: Thursday, June 23, 2005 11:19 AM > >>>>>>>>> To: Suzanna Lewis > >>>>>>>>> Cc: DAS/2 > >>>>>>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > >>>>>>>>> > >>>>>>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby > >>> (3rd > >>>>>>>> > >>>>>>>> floor) > >>>>>>>> > >>>>>>>>> and figure it out from there. > >>>>>>>>> > >>>>>>>>> gregg > >>>>>>>>> > >>>>>>>>>> -----Original Message----- > >>>>>>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] > >>>>>>>>>> Sent: Thursday, June 23, 2005 7:43 AM > >>>>>>>>>> To: Helt,Gregg > >>>>>>>>>> Cc: DAS/2 > >>>>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > >>>>>>>>>> > >>>>>>>>>> Where? > >>>>>>>>>> > >>>>>>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > >>>>>>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. Let > >>> me > >>>>>>>> > >>>>>>>> know > >>>>>>>> > >>>>>>>>>>> what > >>>>>>>>>>> you think. > >>>>>>>>>>> > >>>>>>>>>>> gregg > >>>>>>>>>>> > >>>>>>>>>>> Thursday, June 23 > >>>>>>>>>>> 1:30 PM - 3 PM Retrieval Spec > >>>>>>>>>>> 3:30 PM - 5 PM Registry and Discovery > >>>>>>>>>>> 5 PM - 6 PM Writeback Spec > >>>>>>>>>>> 6 PM - 7 PM Continuation Grant > >>>>>>>>>>> 7:00 PM Dinner > >>>>>>>>>>> > >>>>>>>>>>> Friday, June 24 > >>>>>>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? > >>>>>>>>>>> 5 PM -- ?? DAS/2 BOF > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> _______________________________________________ > >>>>>>>>>>> DAS2 mailing list > >>>>>>>>>>> DAS2 at portal.open-bio.org > >>>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > >>>>>>>>> > >>>>>>>>> _______________________________________________ > >>>>>>>>> DAS2 mailing list > >>>>>>>>> DAS2 at portal.open-bio.org > >>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > >>>>>>>> > >>>>>>>> _______________________________________________ > >>>>>>>> DAS2 mailing list > >>>>>>>> DAS2 at portal.open-bio.org > >>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> DAS2 mailing list > >>>>>>> DAS2 at portal.open-bio.org > >>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > >>>>>> > >>>>>> -- > >>>>>> Lincoln Stein > >>>>>> lstein at cshl.edu > >>>>>> Cold Spring Harbor Laboratory > >>>>>> 1 Bungtown Road > >>>>>> Cold Spring Harbor, NY 11724 > >>>>>> (516) 367-8380 (voice) > >>>>>> (516) 367-8389 (fax) > >>>>>> _______________________________________________ > >>>>>> DAS2 mailing list > >>>>>> DAS2 at portal.open-bio.org > >>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > >>>> > >>>> -- > >>>> Lincoln D. Stein > >>>> Cold Spring Harbor Laboratory > >>>> 1 Bungtown Road > >>>> Cold Spring Harbor, NY 11724 > >>> > >>> _______________________________________________ > >>> DAS2 mailing list > >>> DAS2 at portal.open-bio.org > >>> http://portal.open-bio.org/mailman/listinfo/das2 > >> > >> _______________________________________________ > >> DAS2 mailing list > >> DAS2 at portal.open-bio.org > >> http://portal.open-bio.org/mailman/listinfo/das2 > > From lstein at cshl.edu Mon Jun 27 13:33:04 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 27 Jun 2005 09:33:04 -0400 Subject: [DAS2] DAS/2 meeting schedule for Monday In-Reply-To: References: Message-ID: <200506270933.05116.lstein@cshl.edu> Ok, I'll be there. I'm working on the Reactome grant, so I will probably not be able to attend the entire meeting, but I am keenly interested in hearing what the BOF attendees had to say about querying over ontologies. Lincoln On Sunday 26 June 2005 06:35 pm, Helt,Gregg wrote: > I've reserved a room for a DAS/2 meeting tomorrow (Monday), Duluth (on > the 5th floor), from 2PM to 6PM Eastern time. It also comes with a > better speakerphone than what we had last time. Lincoln and Allen, > please let me know as soon as possible if you can't make it! With a > four hour window, I'm hoping you can both teleconference in for at least > part of the meeting. > > I've also tentatively reserved the same room for 2PM to 5 PM Tuesday, > Eastern time. > > Conference phone #: 800-531-3250 > Conference id: 2879055 > > gregg > > > -----Original Message----- > > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > Sent: Sunday, June 26, 2005 11:29 AM > > To: Chervitz, Steve > > Cc: Helt,Gregg; das2 at portal.open-bio.org > > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > > > No meeting today. Gregg will be back latter today to arrange a room > > for > > > tomorrow and let us know. (appears like my last mail didn't get > > through) > > > > On Jun 26, 2005, at 11:26 AM, Chervitz, Steve wrote: > > > Is there a meeting on for today? Did it happen already? Gregg: Are > > you > > > > going > > > to be back at ISMB today? > > > > > > Steve > > > > > >> From: Suzanna Lewis > > >> Date: Fri, 24 Jun 2005 19:56:23 -0400 > > >> To: "Helt,Gregg" > > >> Cc: > > >> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >> > > >> Ah, I was wondering why I didn't find you there. Sunday morn would > > >> work > > >> for me. > > >> > > >> On Jun 24, 2005, at 7:08 PM, Helt,Gregg wrote: > > >>> Apologies, looks like we lost the room I was planning to meet in > > (and > > > >>> the speakerphone). I think we better reschedule. How about > > starting > > > >>> up > > >>> again on Sunday? > > >>> > > >>> Gregg > > >>> > > >>>> -----Original Message----- > > >>>> From: Lincoln Stein [mailto:lstein at cshl.edu] > > >>>> Sent: Friday, June 24, 2005 2:18 PM > > >>>> To: Helt,Gregg > > >>>> Cc: das2 at portal.open-bio.org > > >>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >>>> > > >>>> Sounds good! > > >>>> > > >>>> Lincoln > > >>>> > > >>>> On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: > > >>>>> Yep, will that work for you? We're holding it in the Ambassador > > II > > > >>> room > > >>> > > >>>>> (where BOSC is), the hotel folks are supposed to install a > > >>> > > >>> speakerphone > > >>> > > >>>>> for us. Same teleconference numbers: > > >>>>> Phone: 800-531-3250 > > >>>>> Id: 2879055 > > >>>>> > > >>>>> thanks, > > >>>>> gregg > > >>>>> > > >>>>>> -----Original Message----- > > >>>>>> From: das2-bounces at portal.open-bio.org > > >>>>> > > >>>>> [mailto:das2-bounces at portal.open- > > >>>>> > > >>>>>> bio.org] On Behalf Of Lincoln Stein > > >>>>>> Sent: Friday, June 24, 2005 11:14 AM > > >>>>>> To: das2 at portal.open-bio.org > > >>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >>>>>> > > >>>>>> Hi, > > >>>>>> > > >>>>>> Are we still on for a DAS meeting (me by telephone) at 7 pm > > this > > > >>>>> evening? > > >>>>> > > >>>>>> Lincoln > > >>>>>> > > >>>>>> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: > > >>>>>>> late breaking news. > > >>>>>>> > > >>>>>>> we're meeting at 2 in room c on the 39th flooor. > > >>>>>>> > > >>>>>>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > > >>>>>>>> Still trying to figure out DAS/2 meeting location today, > > >>> > > >>> hoping to > > >>> > > >>>>>>>> start > > >>>>>>>> around 1:30 PM. Assuming we have access to a phone, for > > those > > > >>> of > > >>> > > >>>>> you > > >>>>> > > >>>>>>>> who need to call in, here's the conference line info: > > >>>>>>>> > > >>>>>>>> Dial-in, domestic: 800-531-3250 > > >>>>>>>> International: 303-928-2693 > > >>>>>>>> Conference ID: 2879055 > > >>>>>>>> > > >>>>>>>> thanks, > > >>>>>>>> gregg > > >>>>>>>> > > >>>>>>>>> -----Original Message----- > > >>>>>>>>> From: das2-bounces at portal.open-bio.org > > >>>>>>>> > > >>>>>>>> [mailto:das2-bounces at portal.open- > > >>>>>>>> > > >>>>>>>>> bio.org] On Behalf Of Helt,Gregg > > >>>>>>>>> Sent: Thursday, June 23, 2005 11:19 AM > > >>>>>>>>> To: Suzanna Lewis > > >>>>>>>>> Cc: DAS/2 > > >>>>>>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > > >>>>>>>>> > > >>>>>>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby > > >>> > > >>> (3rd > > >>> > > >>>>>>>> floor) > > >>>>>>>> > > >>>>>>>>> and figure it out from there. > > >>>>>>>>> > > >>>>>>>>> gregg > > >>>>>>>>> > > >>>>>>>>>> -----Original Message----- > > >>>>>>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > >>>>>>>>>> Sent: Thursday, June 23, 2005 7:43 AM > > >>>>>>>>>> To: Helt,Gregg > > >>>>>>>>>> Cc: DAS/2 > > >>>>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >>>>>>>>>> > > >>>>>>>>>> Where? > > >>>>>>>>>> > > >>>>>>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > > >>>>>>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. > > Let > > > >>> me > > >>> > > >>>>>>>> know > > >>>>>>>> > > >>>>>>>>>>> what > > >>>>>>>>>>> you think. > > >>>>>>>>>>> > > >>>>>>>>>>> gregg > > >>>>>>>>>>> > > >>>>>>>>>>> Thursday, June 23 > > >>>>>>>>>>> 1:30 PM - 3 PM Retrieval Spec > > >>>>>>>>>>> 3:30 PM - 5 PM Registry and Discovery > > >>>>>>>>>>> 5 PM - 6 PM Writeback Spec > > >>>>>>>>>>> 6 PM - 7 PM Continuation Grant > > >>>>>>>>>>> 7:00 PM Dinner > > >>>>>>>>>>> > > >>>>>>>>>>> Friday, June 24 > > >>>>>>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? > > >>>>>>>>>>> 5 PM -- ?? DAS/2 BOF > > >>>>>>>>>>> > > >>>>>>>>>>> > > >>>>>>>>>>> _______________________________________________ > > >>>>>>>>>>> DAS2 mailing list > > >>>>>>>>>>> DAS2 at portal.open-bio.org > > >>>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>>>>> > > >>>>>>>>> _______________________________________________ > > >>>>>>>>> DAS2 mailing list > > >>>>>>>>> DAS2 at portal.open-bio.org > > >>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>>>> > > >>>>>>>> _______________________________________________ > > >>>>>>>> DAS2 mailing list > > >>>>>>>> DAS2 at portal.open-bio.org > > >>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>>> > > >>>>>>> _______________________________________________ > > >>>>>>> DAS2 mailing list > > >>>>>>> DAS2 at portal.open-bio.org > > >>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>> > > >>>>>> -- > > >>>>>> Lincoln Stein > > >>>>>> lstein at cshl.edu > > >>>>>> Cold Spring Harbor Laboratory > > >>>>>> 1 Bungtown Road > > >>>>>> Cold Spring Harbor, NY 11724 > > >>>>>> (516) 367-8380 (voice) > > >>>>>> (516) 367-8389 (fax) > > >>>>>> _______________________________________________ > > >>>>>> DAS2 mailing list > > >>>>>> DAS2 at portal.open-bio.org > > >>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>> > > >>>> -- > > >>>> Lincoln D. Stein > > >>>> Cold Spring Harbor Laboratory > > >>>> 1 Bungtown Road > > >>>> Cold Spring Harbor, NY 11724 > > >>> > > >>> _______________________________________________ > > >>> DAS2 mailing list > > >>> DAS2 at portal.open-bio.org > > >>> http://portal.open-bio.org/mailman/listinfo/das2 > > >> > > >> _______________________________________________ > > >> DAS2 mailing list > > >> DAS2 at portal.open-bio.org > > >> http://portal.open-bio.org/mailman/listinfo/das2 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 -- Lincoln Stein lstein at cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From suzi at fruitfly.org Mon Jun 27 13:57:23 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Mon, 27 Jun 2005 09:57:23 -0400 Subject: [DAS2] DAS/2 meeting schedule for Monday In-Reply-To: <200506270933.05116.lstein@cshl.edu> References: <200506270933.05116.lstein@cshl.edu> Message-ID: <83e2755e1eb5a3f5084233173eaf9374@fruitfly.org> Gregg, I'm in the same dilemma. I must work on the Reactome grant (especially since Lincoln just passed it back to me), but I also would like to hear feedback. I will likely be late (sorry). It sure is a good thing we decided to defer until Nov 1! -S On Jun 27, 2005, at 9:33 AM, Lincoln Stein wrote: > Ok, I'll be there. I'm working on the Reactome grant, so I will > probably not > be able to attend the entire meeting, but I am keenly interested in > hearing > what the BOF attendees had to say about querying over ontologies. > > Lincoln > > > On Sunday 26 June 2005 06:35 pm, Helt,Gregg wrote: >> I've reserved a room for a DAS/2 meeting tomorrow (Monday), Duluth (on >> the 5th floor), from 2PM to 6PM Eastern time. It also comes with a >> better speakerphone than what we had last time. Lincoln and Allen, >> please let me know as soon as possible if you can't make it! With a >> four hour window, I'm hoping you can both teleconference in for at >> least >> part of the meeting. >> >> I've also tentatively reserved the same room for 2PM to 5 PM Tuesday, >> Eastern time. >> >> Conference phone #: 800-531-3250 >> Conference id: 2879055 >> >> gregg >> >>> -----Original Message----- >>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >>> Sent: Sunday, June 26, 2005 11:29 AM >>> To: Chervitz, Steve >>> Cc: Helt,Gregg; das2 at portal.open-bio.org >>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>> >>> No meeting today. Gregg will be back latter today to arrange a room >> >> for >> >>> tomorrow and let us know. (appears like my last mail didn't get >>> through) >>> >>> On Jun 26, 2005, at 11:26 AM, Chervitz, Steve wrote: >>>> Is there a meeting on for today? Did it happen already? Gregg: Are >> >> you >> >>>> going >>>> to be back at ISMB today? >>>> >>>> Steve >>>> >>>>> From: Suzanna Lewis >>>>> Date: Fri, 24 Jun 2005 19:56:23 -0400 >>>>> To: "Helt,Gregg" >>>>> Cc: >>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>> >>>>> Ah, I was wondering why I didn't find you there. Sunday morn would >>>>> work >>>>> for me. >>>>> >>>>> On Jun 24, 2005, at 7:08 PM, Helt,Gregg wrote: >>>>>> Apologies, looks like we lost the room I was planning to meet in >> >> (and >> >>>>>> the speakerphone). I think we better reschedule. How about >> >> starting >> >>>>>> up >>>>>> again on Sunday? >>>>>> >>>>>> Gregg >>>>>> >>>>>>> -----Original Message----- >>>>>>> From: Lincoln Stein [mailto:lstein at cshl.edu] >>>>>>> Sent: Friday, June 24, 2005 2:18 PM >>>>>>> To: Helt,Gregg >>>>>>> Cc: das2 at portal.open-bio.org >>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>>> >>>>>>> Sounds good! >>>>>>> >>>>>>> Lincoln >>>>>>> >>>>>>> On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: >>>>>>>> Yep, will that work for you? We're holding it in the Ambassador >> >> II >> >>>>>> room >>>>>> >>>>>>>> (where BOSC is), the hotel folks are supposed to install a >>>>>> >>>>>> speakerphone >>>>>> >>>>>>>> for us. Same teleconference numbers: >>>>>>>> Phone: 800-531-3250 >>>>>>>> Id: 2879055 >>>>>>>> >>>>>>>> thanks, >>>>>>>> gregg >>>>>>>> >>>>>>>>> -----Original Message----- >>>>>>>>> From: das2-bounces at portal.open-bio.org >>>>>>>> >>>>>>>> [mailto:das2-bounces at portal.open- >>>>>>>> >>>>>>>>> bio.org] On Behalf Of Lincoln Stein >>>>>>>>> Sent: Friday, June 24, 2005 11:14 AM >>>>>>>>> To: das2 at portal.open-bio.org >>>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> Are we still on for a DAS meeting (me by telephone) at 7 pm >> >> this >> >>>>>>>> evening? >>>>>>>> >>>>>>>>> Lincoln >>>>>>>>> >>>>>>>>> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: >>>>>>>>>> late breaking news. >>>>>>>>>> >>>>>>>>>> we're meeting at 2 in room c on the 39th flooor. >>>>>>>>>> >>>>>>>>>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: >>>>>>>>>>> Still trying to figure out DAS/2 meeting location today, >>>>>> >>>>>> hoping to >>>>>> >>>>>>>>>>> start >>>>>>>>>>> around 1:30 PM. Assuming we have access to a phone, for >> >> those >> >>>>>> of >>>>>> >>>>>>>> you >>>>>>>> >>>>>>>>>>> who need to call in, here's the conference line info: >>>>>>>>>>> >>>>>>>>>>> Dial-in, domestic: 800-531-3250 >>>>>>>>>>> International: 303-928-2693 >>>>>>>>>>> Conference ID: 2879055 >>>>>>>>>>> >>>>>>>>>>> thanks, >>>>>>>>>>> gregg >>>>>>>>>>> >>>>>>>>>>>> -----Original Message----- >>>>>>>>>>>> From: das2-bounces at portal.open-bio.org >>>>>>>>>>> >>>>>>>>>>> [mailto:das2-bounces at portal.open- >>>>>>>>>>> >>>>>>>>>>>> bio.org] On Behalf Of Helt,Gregg >>>>>>>>>>>> Sent: Thursday, June 23, 2005 11:19 AM >>>>>>>>>>>> To: Suzanna Lewis >>>>>>>>>>>> Cc: DAS/2 >>>>>>>>>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>>>>>> >>>>>>>>>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby >>>>>> >>>>>> (3rd >>>>>> >>>>>>>>>>> floor) >>>>>>>>>>> >>>>>>>>>>>> and figure it out from there. >>>>>>>>>>>> >>>>>>>>>>>> gregg >>>>>>>>>>>> >>>>>>>>>>>>> -----Original Message----- >>>>>>>>>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] >>>>>>>>>>>>> Sent: Thursday, June 23, 2005 7:43 AM >>>>>>>>>>>>> To: Helt,Gregg >>>>>>>>>>>>> Cc: DAS/2 >>>>>>>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule >>>>>>>>>>>>> >>>>>>>>>>>>> Where? >>>>>>>>>>>>> >>>>>>>>>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: >>>>>>>>>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. >> >> Let >> >>>>>> me >>>>>> >>>>>>>>>>> know >>>>>>>>>>> >>>>>>>>>>>>>> what >>>>>>>>>>>>>> you think. >>>>>>>>>>>>>> >>>>>>>>>>>>>> gregg >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thursday, June 23 >>>>>>>>>>>>>> 1:30 PM - 3 PM Retrieval Spec >>>>>>>>>>>>>> 3:30 PM - 5 PM Registry and Discovery >>>>>>>>>>>>>> 5 PM - 6 PM Writeback Spec >>>>>>>>>>>>>> 6 PM - 7 PM Continuation Grant >>>>>>>>>>>>>> 7:00 PM Dinner >>>>>>>>>>>>>> >>>>>>>>>>>>>> Friday, June 24 >>>>>>>>>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? >>>>>>>>>>>>>> 5 PM -- ?? DAS/2 BOF >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> DAS2 mailing list >>>>>>>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> DAS2 mailing list >>>>>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> DAS2 mailing list >>>>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> DAS2 mailing list >>>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Lincoln Stein >>>>>>>>> lstein at cshl.edu >>>>>>>>> Cold Spring Harbor Laboratory >>>>>>>>> 1 Bungtown Road >>>>>>>>> Cold Spring Harbor, NY 11724 >>>>>>>>> (516) 367-8380 (voice) >>>>>>>>> (516) 367-8389 (fax) >>>>>>>>> _______________________________________________ >>>>>>>>> DAS2 mailing list >>>>>>>>> DAS2 at portal.open-bio.org >>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>>>> >>>>>>> -- >>>>>>> Lincoln D. Stein >>>>>>> Cold Spring Harbor Laboratory >>>>>>> 1 Bungtown Road >>>>>>> Cold Spring Harbor, NY 11724 >>>>>> >>>>>> _______________________________________________ >>>>>> DAS2 mailing list >>>>>> DAS2 at portal.open-bio.org >>>>>> http://portal.open-bio.org/mailman/listinfo/das2 >>>>> >>>>> _______________________________________________ >>>>> DAS2 mailing list >>>>> DAS2 at portal.open-bio.org >>>>> http://portal.open-bio.org/mailman/listinfo/das2 >> >> _______________________________________________ >> DAS2 mailing list >> DAS2 at portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/das2 > > -- > Lincoln Stein > lstein at cshl.edu > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From bugzilla-daemon at portal.open-bio.org Mon Jun 27 19:51:57 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 27 Jun 2005 15:51:57 -0400 Subject: [DAS2] [Bug 1792] allow 'type's which aren't derived from sofa Message-ID: <200506271951.j5RJpvu6009089@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1792 sac at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From sac at bioperl.org 2005-06-27 15:51 ------- We decided by teleconference during ISMB that types for genome-DAS should be restricted to SO. We should include documentation describing what to do if you want to annotate a type in the genome- DAS space that isn't in SO. Something like "either notify the SO curators to get your term added or point to the most general feature in SO that applies, and place your term of interest in an ontology that extends SO, and point to that via RDF. Here's an example...." ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 20:07:58 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:07:58 -0400 Subject: [DAS2] [Bug 1797] don't need compact formats for non-feature requests Message-ID: <200506282007.j5SK7wQw001094@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1797 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|das2 at portal.open-bio.org |dalke at dalkescientific.com ------- Additional Comments From dalke at dalkescientific.com 2005-06-28 16:07 ------- everyone agrees. Remove references from the spec. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 20:32:49 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:32:49 -0400 Subject: [DAS2] [Bug 1799] server should put server type & version in the HTTP headers Message-ID: <200506282032.j5SKWn8L001476@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1799 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|das2 at portal.open-bio.org |dalke at dalkescientific.com ------- Additional Comments From dalke at dalkescientific.com 2005-06-28 16:32 ------- Everyone agrees. Does the HTTP spec suggest the proper header for this? ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 20:36:26 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:36:26 -0400 Subject: [DAS2] [Bug 1803] indicate that two reference coordinate systems are the same Message-ID: <200506282036.j5SKaQ0u001514@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1803 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|das2 at portal.open-bio.org |lstein at cshl.org ------- Additional Comments From dalke at dalkescientific.com 2005-06-28 16:36 ------- Lincoln says that he worked on this and was surprised that it wasn't in the spec. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 20:10:27 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:10:27 -0400 Subject: [DAS2] [Bug 1798] add a subelement to for type-specific format info Message-ID: <200506282010.j5SKARib001137@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1798 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |DUPLICATE ------- Additional Comments From dalke at dalkescientific.com 2005-06-28 16:10 ------- *** This bug has been marked as a duplicate of 1796 *** ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 20:48:00 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:48:00 -0400 Subject: [DAS2] [Bug 1807] Where do seqids come from? Message-ID: <200506282048.j5SKm0Pf001685@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1807 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|das2 at portal.open-bio.org |dalke at dalkescientific.com ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 20:47:47 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:47:47 -0400 Subject: [DAS2] [Bug 1806] When should DAS/2 URLs end with a '/'? Message-ID: <200506282047.j5SKllH6001677@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1806 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- Additional Comments From dalke at dalkescientific.com 2005-06-28 16:47 ------- The Ren Cen Triumvirate has decided here shall be no terminal '/'s on any DAS/2 URLS, though they may be used in xml:base. So mote it be. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 20:50:02 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:50:02 -0400 Subject: [DAS2] [Bug 1808] , region ids and sequence ids Message-ID: <200506282050.j5SKo2xV001746@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1808 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- Additional Comments From dalke at dalkescientific.com 2005-06-28 16:50 ------- We change id in into "seqid" and merge it with the start/end information to make a new URL. Example ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Jun 28 20:50:30 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 28 Jun 2005 16:50:30 -0400 Subject: [DAS2] [Bug 1808] , region ids and sequence ids Message-ID: <200506282050.j5SKoUXW001765@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1808 dalke at dalkescientific.com changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|das2 at portal.open-bio.org |lstein at cshl.org Status|ASSIGNED |NEW ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From lstein at cshl.edu Thu Jun 30 17:50:00 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 30 Jun 2005 13:50:00 -0400 Subject: [DAS2] DAS/2 meeting schedule for Monday In-Reply-To: References: Message-ID: <200506301350.00937.lstein@cshl.edu> Hello, I won't be able to participate in today's conference call (if there is one) due to time pressures on getting the Reactome grant out the door. Lincoln On Sunday 26 June 2005 06:35 pm, Helt,Gregg wrote: > I've reserved a room for a DAS/2 meeting tomorrow (Monday), Duluth (on > the 5th floor), from 2PM to 6PM Eastern time. It also comes with a > better speakerphone than what we had last time. Lincoln and Allen, > please let me know as soon as possible if you can't make it! With a > four hour window, I'm hoping you can both teleconference in for at least > part of the meeting. > > I've also tentatively reserved the same room for 2PM to 5 PM Tuesday, > Eastern time. > > Conference phone #: 800-531-3250 > Conference id: 2879055 > > gregg > > > -----Original Message----- > > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > Sent: Sunday, June 26, 2005 11:29 AM > > To: Chervitz, Steve > > Cc: Helt,Gregg; das2 at portal.open-bio.org > > Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > > > No meeting today. Gregg will be back latter today to arrange a room > > for > > > tomorrow and let us know. (appears like my last mail didn't get > > through) > > > > On Jun 26, 2005, at 11:26 AM, Chervitz, Steve wrote: > > > Is there a meeting on for today? Did it happen already? Gregg: Are > > you > > > > going > > > to be back at ISMB today? > > > > > > Steve > > > > > >> From: Suzanna Lewis > > >> Date: Fri, 24 Jun 2005 19:56:23 -0400 > > >> To: "Helt,Gregg" > > >> Cc: > > >> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >> > > >> Ah, I was wondering why I didn't find you there. Sunday morn would > > >> work > > >> for me. > > >> > > >> On Jun 24, 2005, at 7:08 PM, Helt,Gregg wrote: > > >>> Apologies, looks like we lost the room I was planning to meet in > > (and > > > >>> the speakerphone). I think we better reschedule. How about > > starting > > > >>> up > > >>> again on Sunday? > > >>> > > >>> Gregg > > >>> > > >>>> -----Original Message----- > > >>>> From: Lincoln Stein [mailto:lstein at cshl.edu] > > >>>> Sent: Friday, June 24, 2005 2:18 PM > > >>>> To: Helt,Gregg > > >>>> Cc: das2 at portal.open-bio.org > > >>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >>>> > > >>>> Sounds good! > > >>>> > > >>>> Lincoln > > >>>> > > >>>> On Friday 24 June 2005 04:45 pm, Helt,Gregg wrote: > > >>>>> Yep, will that work for you? We're holding it in the Ambassador > > II > > > >>> room > > >>> > > >>>>> (where BOSC is), the hotel folks are supposed to install a > > >>> > > >>> speakerphone > > >>> > > >>>>> for us. Same teleconference numbers: > > >>>>> Phone: 800-531-3250 > > >>>>> Id: 2879055 > > >>>>> > > >>>>> thanks, > > >>>>> gregg > > >>>>> > > >>>>>> -----Original Message----- > > >>>>>> From: das2-bounces at portal.open-bio.org > > >>>>> > > >>>>> [mailto:das2-bounces at portal.open- > > >>>>> > > >>>>>> bio.org] On Behalf Of Lincoln Stein > > >>>>>> Sent: Friday, June 24, 2005 11:14 AM > > >>>>>> To: das2 at portal.open-bio.org > > >>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >>>>>> > > >>>>>> Hi, > > >>>>>> > > >>>>>> Are we still on for a DAS meeting (me by telephone) at 7 pm > > this > > > >>>>> evening? > > >>>>> > > >>>>>> Lincoln > > >>>>>> > > >>>>>> On Thursday 23 June 2005 01:45 pm, Suzanna Lewis wrote: > > >>>>>>> late breaking news. > > >>>>>>> > > >>>>>>> we're meeting at 2 in room c on the 39th flooor. > > >>>>>>> > > >>>>>>> On Jun 23, 2005, at 12:05 PM, Helt,Gregg wrote: > > >>>>>>>> Still trying to figure out DAS/2 meeting location today, > > >>> > > >>> hoping to > > >>> > > >>>>>>>> start > > >>>>>>>> around 1:30 PM. Assuming we have access to a phone, for > > those > > > >>> of > > >>> > > >>>>> you > > >>>>> > > >>>>>>>> who need to call in, here's the conference line info: > > >>>>>>>> > > >>>>>>>> Dial-in, domestic: 800-531-3250 > > >>>>>>>> International: 303-928-2693 > > >>>>>>>> Conference ID: 2879055 > > >>>>>>>> > > >>>>>>>> thanks, > > >>>>>>>> gregg > > >>>>>>>> > > >>>>>>>>> -----Original Message----- > > >>>>>>>>> From: das2-bounces at portal.open-bio.org > > >>>>>>>> > > >>>>>>>> [mailto:das2-bounces at portal.open- > > >>>>>>>> > > >>>>>>>>> bio.org] On Behalf Of Helt,Gregg > > >>>>>>>>> Sent: Thursday, June 23, 2005 11:19 AM > > >>>>>>>>> To: Suzanna Lewis > > >>>>>>>>> Cc: DAS/2 > > >>>>>>>>> Subject: RE: [DAS2] Tentative DAS/2 meeting schedule > > >>>>>>>>> > > >>>>>>>>> Not sure yet. Let's meet at 1:30 PM in the main hotel lobby > > >>> > > >>> (3rd > > >>> > > >>>>>>>> floor) > > >>>>>>>> > > >>>>>>>>> and figure it out from there. > > >>>>>>>>> > > >>>>>>>>> gregg > > >>>>>>>>> > > >>>>>>>>>> -----Original Message----- > > >>>>>>>>>> From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > >>>>>>>>>> Sent: Thursday, June 23, 2005 7:43 AM > > >>>>>>>>>> To: Helt,Gregg > > >>>>>>>>>> Cc: DAS/2 > > >>>>>>>>>> Subject: Re: [DAS2] Tentative DAS/2 meeting schedule > > >>>>>>>>>> > > >>>>>>>>>> Where? > > >>>>>>>>>> > > >>>>>>>>>> On Jun 22, 2005, at 3:04 PM, Helt,Gregg wrote: > > >>>>>>>>>>> Proposed schedule for DAS/2 mini-meeting at BOSC 2005. > > Let > > > >>> me > > >>> > > >>>>>>>> know > > >>>>>>>> > > >>>>>>>>>>> what > > >>>>>>>>>>> you think. > > >>>>>>>>>>> > > >>>>>>>>>>> gregg > > >>>>>>>>>>> > > >>>>>>>>>>> Thursday, June 23 > > >>>>>>>>>>> 1:30 PM - 3 PM Retrieval Spec > > >>>>>>>>>>> 3:30 PM - 5 PM Registry and Discovery > > >>>>>>>>>>> 5 PM - 6 PM Writeback Spec > > >>>>>>>>>>> 6 PM - 7 PM Continuation Grant > > >>>>>>>>>>> 7:00 PM Dinner > > >>>>>>>>>>> > > >>>>>>>>>>> Friday, June 24 > > >>>>>>>>>>> 1:30 PM - 4:30 PM Anything we didn't cover in first day? > > >>>>>>>>>>> 5 PM -- ?? DAS/2 BOF > > >>>>>>>>>>> > > >>>>>>>>>>> > > >>>>>>>>>>> _______________________________________________ > > >>>>>>>>>>> DAS2 mailing list > > >>>>>>>>>>> DAS2 at portal.open-bio.org > > >>>>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>>>>> > > >>>>>>>>> _______________________________________________ > > >>>>>>>>> DAS2 mailing list > > >>>>>>>>> DAS2 at portal.open-bio.org > > >>>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>>>> > > >>>>>>>> _______________________________________________ > > >>>>>>>> DAS2 mailing list > > >>>>>>>> DAS2 at portal.open-bio.org > > >>>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>>> > > >>>>>>> _______________________________________________ > > >>>>>>> DAS2 mailing list > > >>>>>>> DAS2 at portal.open-bio.org > > >>>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>>>> > > >>>>>> -- > > >>>>>> Lincoln Stein > > >>>>>> lstein at cshl.edu > > >>>>>> Cold Spring Harbor Laboratory > > >>>>>> 1 Bungtown Road > > >>>>>> Cold Spring Harbor, NY 11724 > > >>>>>> (516) 367-8380 (voice) > > >>>>>> (516) 367-8389 (fax) > > >>>>>> _______________________________________________ > > >>>>>> DAS2 mailing list > > >>>>>> DAS2 at portal.open-bio.org > > >>>>>> http://portal.open-bio.org/mailman/listinfo/das2 > > >>>> > > >>>> -- > > >>>> Lincoln D. Stein > > >>>> Cold Spring Harbor Laboratory > > >>>> 1 Bungtown Road > > >>>> Cold Spring Harbor, NY 11724 > > >>> > > >>> _______________________________________________ > > >>> DAS2 mailing list > > >>> DAS2 at portal.open-bio.org > > >>> http://portal.open-bio.org/mailman/listinfo/das2 > > >> > > >> _______________________________________________ > > >> DAS2 mailing list > > >> DAS2 at portal.open-bio.org > > >> http://portal.open-bio.org/mailman/listinfo/das2 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724