From postmaster at diplobel.org Mon Feb 2 05:42:52 2004 From: postmaster at diplobel.org (System Administrator) Date: Mon Feb 2 05:53:07 2004 Subject: [MOBY-dev] Undeliverable: hello Message-ID: <8A1A6B6EE755D411ADB20050041783100249708E@PHOEBE> Your message To: adam@diplobel.org Subject: hello Sent: Mon, 2 Feb 2004 05:46:34 -0500 did not reach the following recipient(s): adam@diplobel.org on Mon, 2 Feb 2004 05:42:50 -0500 The recipient name is not recognized The MTS-ID of the original message is: c=us;a= ;p=diplobel;l=PHOEBE0402021042D0G4JNVC MSEXCH:IMS:Diplobel:DIPLOBEL:PHOEBE 0 (000C05A6) Unknown Recipient From bdfy at hotmail.com Mon Feb 2 19:10:15 2004 From: bdfy at hotmail.com (bdfy@hotmail.com) Date: Mon Feb 2 19:16:36 2004 Subject: [MOBY-dev] Hi Message-ID: <200402030016.i130GSEs029932@portal.open-bio.org> From postmaster at diplobel.org Mon Feb 2 19:06:58 2004 From: postmaster at diplobel.org (System Administrator) Date: Mon Feb 2 19:17:06 2004 Subject: [MOBY-dev] Undeliverable: hi Message-ID: <8A1A6B6EE755D411ADB200500417831002515F8A@PHOEBE> Your message To: adam@diplobel.org Subject: hi Sent: Mon, 2 Feb 2004 19:10:49 -0500 did not reach the following recipient(s): adam@diplobel.org on Mon, 2 Feb 2004 19:06:54 -0500 The recipient name is not recognized The MTS-ID of the original message is: c=us;a= ;p=diplobel;l=PHOEBE04020300061FMDK4S3 MSEXCH:IMS:Diplobel:DIPLOBEL:PHOEBE 0 (000C05A6) Unknown Recipient From postmaster at diplobel.org Tue Feb 3 04:50:14 2004 From: postmaster at diplobel.org (System Administrator) Date: Tue Feb 3 05:00:21 2004 Subject: [MOBY-dev] Undeliverable: Error Message-ID: <8A1A6B6EE755D411ADB200500417831002507A05@PHOEBE> Your message To: steve@diplobel.org Subject: Error Sent: Tue, 3 Feb 2004 04:54:01 -0500 did not reach the following recipient(s): steve@diplobel.org on Tue, 3 Feb 2004 04:50:09 -0500 The recipient name is not recognized The MTS-ID of the original message is: c=us;a= ;p=diplobel;l=PHOEBE04020309501FMDK7KB MSEXCH:IMS:Diplobel:DIPLOBEL:PHOEBE 0 (000C05A6) Unknown Recipient From MAILER-DAEMON at mail1.chek.com Fri Feb 6 08:12:10 2004 From: MAILER-DAEMON at mail1.chek.com (MAILER-DAEMON@mail1.chek.com) Date: Fri Feb 6 08:18:17 2004 Subject: [MOBY-dev] failure notice Message-ID: <200402061318.i16DIDHH017661@portal.open-bio.org> Hi. This is the qmail-send program at mail1.chek.com. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : User's Disk Quota Exceeded. Sorry, your message cannot be delivered as the recipient has exceeded their disk space limit for email. --- Below this line is a copy of the message. Return-Path: Received: (qmail 32631 invoked by uid 0); 6 Feb 2004 13:12:08 -0000 Received: from 212.68.223.9.brutele.be (HELO biomoby.org) (212.68.223.9) by maude.synacor.com with SMTP; 6 Feb 2004 13:12:08 -0000 From: moby-dev@biomoby.org To: jimmy@freeze.com Subject: Mail Transaction Failed Date: Fri, 6 Feb 2004 14:12:22 +0100 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0013_FA914C66.354BE840" X-Priority: 3 X-MSMail-Priority: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0013_FA914C66.354BE840 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit ҇Ea {A0 dȸ{;[|1-v*NEb"c'٪2R(wAb&Ğ$ ((2F* uAHqLerM\D ?"Nm;$^1CRZÅrݱߐ]{𐗜ĂtZkitۛ}Z%I\m|!bИLO^|SᇛU(Mj8-2".TxTmS#TT-v0;(Wij LhEU2/2ݣdW_]g]9dFd8ʦv1dIxWhb%K2i&qNSE2ޤxCVd3` \;O㲱$όwxkm{pa][ՎW0lHuj'wLЪlD[n1ZOn8i!LKN#3mrS|FU|#]4NFK&W6;lpV9>W5-Hb'fK_ãi-tyq?i8fEO_Eq'}S5-N97)y) 7M#Ry'ǸZMGMN%7ly|?:o.g-B#0r&-CzG؍T}p/JJj]!qnmJucy8iJk&ipNI徱hTf|)oϟ Ǔr|Xa-Sth 5U;9{:gDKCӱ8Ĭ~_:ҮKƣ/td#ߣ~KtuV;B! :6,DuR/ ̩<2VyFbd,jk,lcŲc&&db-oQjr48hh n*0Pfohc:ƧM0qugLt#쐳b7Lg4<Ƨp?#dë[ELc[»~ߚWL:Z0юDOY:}v-i2[SՒB`Wn6x0~vqcRHTuyB%gUBASߥ~^S3(Ѯlϐ3ؖFrSރc5kI`)h2%ypR\ fyC3ʻςnq-w٣AZ5F gѩ`&y_-/NϹCe'JU#N{9ևa0h:>0WSK詈hP)#FVosF>/s?T8ǟh~A̘40},yεKKEk/!OX5|7NG>tY0ιaacyK񩽊8㦮`ݵ::dmftP}Rwc$z2)olm0-VZ[YiFl!-K$|MؑՏu.՜MNRuo4:__ ()c!2엻x3Oq74F3cGTfm!;HZ$a41Ct0ȎS];AV~^&q[֡c\)jv Wouldn't y'know it, a big virus attack right when I have no access to the net! Sorry about all the crap that came over moby-guts last week! I've just set it to subscriber-only postings, so that should solve the problem. If you have problems with your commits not getting posted to the list please let me know. It does mean, I believe, that you will need to subscribe to the -guts list in order for your commit logs to be posted... Developers, if you haven't done so, please do! Cheers! Mark -- Mark Wilkinson, Assistant Professor (Bioinformatics) Dept. of Medical Genetics, University of British Columbia James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research 166 - 1081 Burrard St., Vancouver, BC, Canada, V6Z 1Y6 ------------------------------------------------------------------------ It just goes to show you that SOAP::Lite is more intuitive than you might think, if you know enough Perl and have the patience to dive into the source code. -Byrne Reese -http://builder.com.com/5100-6389_14-1045078-2.html ------------------------------------------------------------------------ From senger at ebi.ac.uk Wed Feb 11 19:08:23 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Wed Feb 11 19:14:23 2004 Subject: [MOBY-dev] case-sensitivity In-Reply-To: <1068411475.1706.23.camel@localhost.localdomain> Message-ID: Mark, Today Rebecca pointed me out that there are problems with the Moby Graphs. And, indeed, there are. Not only for her Moby server - but also for the main Moby server. I am looking into it now - but the first thing which seems to be obviously wrong (they may be others) is about case-sensitivity of entity names. I will tell you what I see and you wil tell me if it is normal, strange or wrong. Let's talk about data types (I assume that the same can be seen by other entities as well but I have not checked): If I ask for all data types names ('retrieveObjectNames') I am getting (for example for a string data type): So far, so good. If I ask for its definition ('retrieveObjectDefinition') I am getting: urn:lsid:biomoby.org:objectclass:String .... Which seems okay because both methods returned 'String' (one as the whole name, the second one as a last part of an LSID). But if I do the same thing with the Rebecca's server, I get first 'String' but the 'retrieveObjectDefinition' returns: urn:lsid:biomoby.org:objectclass:string Notice that now the last part of the LSID is 'string' with lower-case. The LSID specification explicitly says that starting from the 'namespace' field it is case-sensitive. However, perhaps BioMoby does not care and treats LSID as case-insensitive (meaning actually that it recognizes the same object under many different LSIDs - differing by the cases). Is this the case? Or does Rebecca's server do something wrong? When this is answered and discussed I will look further why graphs are not being created properly... Thanks, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Wed Feb 11 17:20:28 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Feb 11 19:27:34 2004 Subject: [MOBY] [MOBY-dev] case-sensitivity In-Reply-To: References: Message-ID: <1076538028.1677.134.camel@localilluminae.com> Hi all, It is likely that Rebecca needs to update her database. As soon as Sean M. gave me assurances that the bug in the LSID stack that forced lower-case ID's had been fixed, I then went into the database by hand and changed all of the entries such that the LSID and the Objectname had the same case (as you and others had requested). This is how it was meant to be in the first place, but the bug had mucked things up such that the LSID's all had to be lower case regardless of the case of the original name of the Object (or service, or namespace). M On Wed, 2004-02-11 at 18:08, Martin Senger wrote: > Mark, > Today Rebecca pointed me out that there are problems with the Moby > Graphs. And, indeed, there are. Not only for her Moby server - but also > for the main Moby server. > I am looking into it now - but the first thing which seems to be > obviously wrong (they may be others) is about case-sensitivity of entity > names. I will tell you what I see and you wil tell me if it is normal, > strange or wrong. > Let's talk about data types (I assume that the same can be seen by > other entities as well but I have not checked): > If I ask for all data types names ('retrieveObjectNames') I am getting > (for example for a string data type): > > > > > > So far, so good. > If I ask for its definition ('retrieveObjectDefinition') I am getting: > > > urn:lsid:biomoby.org:objectclass:String > > .... > > > Which seems okay because both methods returned 'String' (one as the > whole name, the second one as a last part of an LSID). But if I do the > same thing with the Rebecca's server, I get first 'String' but the > 'retrieveObjectDefinition' returns: > > urn:lsid:biomoby.org:objectclass:string > > Notice that now the last part of the LSID is 'string' with lower-case. > > The LSID specification explicitly says that starting from the > 'namespace' field it is case-sensitive. However, perhaps BioMoby does not > care and treats LSID as case-insensitive (meaning actually that it > recognizes the same object under many different LSIDs - differing by the > cases). Is this the case? Or does Rebecca's server do something wrong? > > When this is answered and discussed I will look further why graphs are > not being created properly... > > Thanks, > Martin -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Wed Feb 11 19:31:21 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Wed Feb 11 19:37:19 2004 Subject: [MOBY] [MOBY-dev] case-sensitivity In-Reply-To: <1076538028.1677.134.camel@localilluminae.com> Message-ID: > This is how it was meant to be in the first place... > I am happy with this answer - what you said what exactly what I hope for :-) Rebecca, there may still be some other problems with graphs - I will investigate further, but perhaps you may try again after you update your database... (and let me know please) Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Wed Feb 11 17:55:06 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Feb 11 20:02:16 2004 Subject: [MOBY] [MOBY-dev] case-sensitivity In-Reply-To: References: Message-ID: <1076540106.1677.149.camel@localilluminae.com> Ughh.... Rebecca is going to KILL me next week in Madrid! She HATES it when I give her more work to do! ;-) M On Wed, 2004-02-11 at 18:31, Martin Senger wrote: > > This is how it was meant to be in the first place... > > > I am happy with this answer - what you said what exactly what I hope > for :-) > Rebecca, there may still be some other problems with graphs - I will > investigate further, but perhaps you may try again after you update your > database... (and let me know please) > > Martin -- Mark Wilkinson Illuminae From lstein at cshl.edu Fri Feb 13 10:57:37 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri Feb 13 11:04:37 2004 Subject: [MOBY-dev] Fwd: [MOBY-l] Proposed dates for MOBY meeting Message-ID: <200402131757.37271.lstein@cshl.edu> -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From markw at illuminae.com Fri Feb 13 11:55:14 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Feb 13 12:01:06 2004 Subject: [MOBY-dev] [Fwd: Re: [MOBY] Re: [MOBY-l] Proposed dates for MOBY meeting] Message-ID: <1076691314.2024.16.camel@localilluminae.com> flipping this conversation over to the correct list... Hi Lincoln! Thanks for the invitation! I could probably swing it for April as well. The earlier dates are much better for me also. Mark On Fri, 2004-02-13 at 10:21, Martin Senger wrote: > > On Fri, 2004-02-13 at 10:21, Lincoln Stein wrote: > > How about the weekends of April 3-4 or April 10-11 for the next MOBY > > meeting? > > > 3-4 April much better, because April 9-12 are Easter Holidays > Martin -- Mark Wilkinson Illuminae From lstein at cshl.edu Mon Feb 16 04:47:39 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon Feb 16 04:53:37 2004 Subject: [MOBY-dev] Re: [MOBY-l] Proposed dates for MOBY meeting In-Reply-To: <1509.200.71.12.137.1076794531.squirrel@uhura.sdsc.edu> References: <200402131733.08070.lstein@cshl.edu> <1509.200.71.12.137.1076794531.squirrel@uhura.sdsc.edu> Message-ID: <200402161147.39223.lstein@cshl.edu> OK, it looks like we're on for the April 3-4 dates. Please send me a list of the number of people from your group who will be attending and I will make the arrangements. Lincoln On Saturday 14 February 2004 11:35 pm, steube@sdsc.edu wrote: > Hi all from Montevideo, Uruguay. I gave a MOBY presentation earlier > this week and next another next week. > > Apr 3, 4 sounds good to me and Gribskov can probably attend, too. > > Ken > > > Hi, > > > > How about the weekends of April 3-4 or April 10-11 for the next > > MOBY meeting? I would be happy to host it at CSHL. Before that > > I'm pretty busy with various meetings, and after that Gary is > > traveling. > > > > Lincoln > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > _______________________________________________ > > moby-l mailing list > > moby-l@biomoby.org > > http://biomoby.org/mailman/listinfo/moby-l -- Lincoln D. 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Powered by Benchmarkemail http://www.benchmarkemail.com REPORT ABUSE http://www.benchmarkemail.com/link/report_abuse.asp?   From markw at illuminae.com Thu Feb 19 01:20:50 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu Feb 19 03:29:53 2004 Subject: [MOBY-dev] Uruguay hits the webstats :-) Message-ID: <1077171650.2062.30.camel@localilluminae.com> Hey Ken et al. Uruguay is now a peculiar blip in the web stats for MOBY Central :-) http://mobycentral.cbr.nrc.ca/AccessLog.html#dom the Canadian accesses are primarily the moby client talking to moby central. The German/Spanish/UK accesses are probably (??) mostly the PlaNet consortium, with the notable exception of Martin's accesses from ebi. Then there is Uruguay - a funny little blip on the map! It made me chuckle :-) Interesting stats, though... e.g. >10,000 requests from PlaNet(?) in just 49 days... and that is an underestimate since they have their own MOBY Central installed at MIPS. Heiko/Rebecca - does your embedded client make *any* of its calls to the public registry, or are they all to your own? Do you have any embedded calls to any of my services running from MOBY Central? I'm just trying to understand whether the European calls are coming primarily from you, or if there is another group(s) using MOBY heavily over there that I am not aware of...?? Another interesting bit of information in there is farther down the page http://mobycentral.cbr.nrc.ca/AccessLog.html#req We will be able to track which objects are most often used, since the ontology server makes calls to retrieve the LSID for the various object types, and this shows up in the GET string :-) Mark -- Mark Wilkinson, Assistant Professor (Bioinformatics) Dept. of Medical Genetics, University of British Columbia James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research 166 - 1081 Burrard St. Vancouver, BC, Canada, V6Z 1Y6 tel: (604) 806 2129 fax: (604) 806 9274 ------------------------------------------------------------------------ It just goes to show you that SOAP::Lite is more intuitive than you might think, if you know enough Perl and have the patience to dive into the source code. -Byrne Reese -http://builder.com.com/5100-6389_14-1045078-2.html ------------------------------------------------------------------------ From markw at illuminae.com Mon Feb 23 16:35:55 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Mon Feb 23 16:42:03 2004 Subject: [MOBY-dev] whitespace in MOBY Objects Message-ID: <1077572155.1643.107.camel@localilluminae.com> Dave Waddell pointed out to me last week that the output from some of my services doesn't parse "nicely" - in particular, when I am passing back e.g. a genbank flat file, along with cross-references, the XML parsers may (in some Perl parsers this is a switchable option) interpret newlines and tabs as whitespace. Thus my output: genbank flatfile here _______ _______ _______ _______ is actually parsed to the following string: " genbank flatfile here _________ _________ _________ _________ " which is obviously not a valid genbank file format! I have just updated my services to be less cavalier about whitespace, but we should probably all look at our services and do the same. This is only important w.r.t. objects that inherit from one of the primitives (String, Integer, etc), since other objects by definition are NOT allowed to have literal content, but it is probably good practice to not be thinking about human readability when constructing our output. I will probably migrate all of my services to use an XML-DOM builder, rather than writing out the XML by hand in the future to ensure that I don't do this by accident. Thanks for the heads-up Dave! Mark -- Mark Wilkinson Illuminae From markw at illuminae.com Wed Feb 25 20:16:33 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Feb 25 20:22:33 2004 Subject: [MOBY-dev] Acknowledging MOBY-S in your code and on your pages Message-ID: <1077758193.1916.43.camel@localilluminae.com> Hi all, In an effort to get a more accurate measure of "impact" for the granting agencies, I have made a "powered by" icon. I would greatly appreciate it if anyone who is building web pages that include content derived by calls to MOBY Central or MOBY Services could link to this icon so that I can measure hits/distribution. http://www.biomoby.org/link_to_us.html Thanks a lot everyone! Mark -- Mark Wilkinson, Assistant Professor (Bioinformatics) Dept. of Medical Genetics, University of British Columbia James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research 166 - 1081 Burrard St. Vancouver, BC, Canada, V6Z 1Y6 tel: (604) 682 2344 ext. 62129 fax: (604) 806 9274 ------------------------------------------------------------------------ It just goes to show you that SOAP::Lite is more intuitive than you might think, if you know enough Perl and have the patience to dive into the source code. -Byrne Reese -http://builder.com.com/5100-6389_14-1045078-2.html ------------------------------------------------------------------------ From lstein at cshl.edu Fri Feb 27 10:40:49 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri Feb 27 10:47:00 2004 Subject: [MOBY-dev] April 3-4 meeting In-Reply-To: <1077758193.1916.43.camel@localilluminae.com> References: <1077758193.1916.43.camel@localilluminae.com> Message-ID: <200402271740.49773.lstein@cshl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I am waiting for CSHL to get back to me on the availability of housing and rooms, but should know early next week whether I can confirm the April 3-4 dates. Lincoln - -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) iD8DBQFAP2UB0CIvUP7P+AkRAoN3AJ0TkJBdreyQX4wH6PvlGiUVoX+CSACfb180 gbFv0o1B6DxN8GHZVLqr5dY= =ZEuI -----END PGP SIGNATURE----- From lstein at cshl.edu Fri Feb 27 10:40:49 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri Feb 27 10:47:00 2004 Subject: [MOBY-dev] April 3-4 meeting In-Reply-To: <1077758193.1916.43.camel@localilluminae.com> References: <1077758193.1916.43.camel@localilluminae.com> Message-ID: <200402271740.49773.lstein@cshl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I am waiting for CSHL to get back to me on the availability of housing and rooms, but should know early next week whether I can confirm the April 3-4 dates. Lincoln - -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) iD8DBQFAP2UB0CIvUP7P+AkRAoN3AJ0TkJBdreyQX4wH6PvlGiUVoX+CSACfb180 gbFv0o1B6DxN8GHZVLqr5dY= =ZEuI -----END PGP SIGNATURE----- From markw at illuminae.com Fri Feb 27 19:00:22 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Feb 27 19:06:21 2004 Subject: [MOBY-dev] For those interested in RDF Message-ID: <1077926422.1910.110.camel@localilluminae.com> Hi all, http://biomoby.org/cgi-bin/RESOURCES/MOBY-S/FULL I've just finished putting together version 2 of the RDF graph of MOBY Central. This should make the "purists" a bit happier since the resources in this graph actually point to other RDF graphs (rather than being LSID's as they were in the first version), and more importantly I am only using my own predicates when I absolutely have to. I still haven't found a way of representing the HAS* relationships using traditional RDF predicates, so anyone who wants to send some suggestions to the list in this regard is more than welcome. All graphs are auto-generated from the RESOURCES script, so they should be up-to-date with the registry at all times. Damian, what would I need to add to this in order for you to query it in a useful way? Does this bring us any closer to "grand unification" or are we still worlds apart? w.r.t. MOBY Objects - I've written a few quick n dirty scripts that convince me that it should be possible to (easily!) auto-convert instantiated MOBY Objects into an equivalent RDF representation... it occurred to me while writing these that MOBY Objects ~fulfil the failed promise of XML - that it should be self-describing data. The MOBY-S object structure is so tightly intertwined with the ontology that representing objects is as easy as generating the RDF graph of the ontology itself! Anyway, if this is true, this might also help in bridging the gap between MOBYShMOBY... Anyway, just random thoughts on a Friday afternoon. I go beer now. Any comments on the RDF are welcome! especially if you find errors (logical or technical). Have a great weekend everyone! Mark -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From bichnguyen at Att.net Sun Feb 29 18:22:23 2004 From: bichnguyen at Att.net (bichnguyen@Att.net) Date: Sun Feb 29 18:24:12 2004 Subject: [MOBY-dev] Registration confirmation Message-ID: Subj From postmaster at diplobel.org Mon Feb 2 05:42:52 2004 From: postmaster at diplobel.org (System Administrator) Date: Mon, 2 Feb 2004 05:42:52 -0500 Subject: [MOBY-dev] Undeliverable: hello Message-ID: <8A1A6B6EE755D411ADB20050041783100249708E@PHOEBE> Your message To: adam at diplobel.org Subject: hello Sent: Mon, 2 Feb 2004 05:46:34 -0500 did not reach the following recipient(s): adam at diplobel.org on Mon, 2 Feb 2004 05:42:50 -0500 The recipient name is not recognized The MTS-ID of the original message is: c=us;a= ;p=diplobel;l=PHOEBE0402021042D0G4JNVC MSEXCH:IMS:Diplobel:DIPLOBEL:PHOEBE 0 (000C05A6) Unknown Recipient From bdfy at hotmail.com Mon Feb 2 19:10:15 2004 From: bdfy at hotmail.com (bdfy@hotmail.com) Date: Tue, 3 Feb 2004 01:10:15 +0100 Subject: [MOBY-dev] Hi Message-ID: <200402030016.i130GSEs029932@portal.open-bio.org> From postmaster at diplobel.org Mon Feb 2 19:06:58 2004 From: postmaster at diplobel.org (System Administrator) Date: Mon, 2 Feb 2004 19:06:58 -0500 Subject: [MOBY-dev] Undeliverable: hi Message-ID: <8A1A6B6EE755D411ADB200500417831002515F8A@PHOEBE> Your message To: adam at diplobel.org Subject: hi Sent: Mon, 2 Feb 2004 19:10:49 -0500 did not reach the following recipient(s): adam at diplobel.org on Mon, 2 Feb 2004 19:06:54 -0500 The recipient name is not recognized The MTS-ID of the original message is: c=us;a= ;p=diplobel;l=PHOEBE04020300061FMDK4S3 MSEXCH:IMS:Diplobel:DIPLOBEL:PHOEBE 0 (000C05A6) Unknown Recipient From postmaster at diplobel.org Tue Feb 3 04:50:14 2004 From: postmaster at diplobel.org (System Administrator) Date: Tue, 3 Feb 2004 04:50:14 -0500 Subject: [MOBY-dev] Undeliverable: Error Message-ID: <8A1A6B6EE755D411ADB200500417831002507A05@PHOEBE> Your message To: steve at diplobel.org Subject: Error Sent: Tue, 3 Feb 2004 04:54:01 -0500 did not reach the following recipient(s): steve at diplobel.org on Tue, 3 Feb 2004 04:50:09 -0500 The recipient name is not recognized The MTS-ID of the original message is: c=us;a= ;p=diplobel;l=PHOEBE04020309501FMDK7KB MSEXCH:IMS:Diplobel:DIPLOBEL:PHOEBE 0 (000C05A6) Unknown Recipient From MAILER-DAEMON at mail1.chek.com Fri Feb 6 08:12:10 2004 From: MAILER-DAEMON at mail1.chek.com (MAILER-DAEMON@mail1.chek.com) Date: 6 Feb 2004 13:12:10 -0000 Subject: [MOBY-dev] failure notice Message-ID: <200402061318.i16DIDHH017661@portal.open-bio.org> Hi. This is the qmail-send program at mail1.chek.com. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : User's Disk Quota Exceeded. Sorry, your message cannot be delivered as the recipient has exceeded their disk space limit for email. --- Below this line is a copy of the message. Return-Path: Received: (qmail 32631 invoked by uid 0); 6 Feb 2004 13:12:08 -0000 Received: from 212.68.223.9.brutele.be (HELO biomoby.org) (212.68.223.9) by maude.synacor.com with SMTP; 6 Feb 2004 13:12:08 -0000 From: moby-dev at biomoby.org To: jimmy at freeze.com Subject: Mail Transaction Failed Date: Fri, 6 Feb 2004 14:12:22 +0100 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0013_FA914C66.354BE840" X-Priority: 3 X-MSMail-Priority: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0013_FA914C66.354BE840 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit ҇Ea {A0 dȸ{;[|1-v*NEb"c'٪2R(wAb&Ğ$ ((2F* uAHqLerM\D ?"Nm;$^1CRZÅrݱߐ]{𐗜ĂtZkitۛ}Z%I\m|!bИLO^|SᇛU(Mj8-2".TxTmS#TT-v0;(Wij LhEU2/2ݣdW_]g]9dFd8ʦv1dIxWhb%K2i&qNSE2ޤxCVd3` \;O㲱$όwxkm{pa][ՎW0lHuj'wLЪlD[n1ZOn8i!LKN#3mrS|FU|#]4NFK&W6;lpV9>W5-Hb'fK_ãi-tyq?i8fEO_Eq'}S5-N97)y) 7M#Ry'ǸZMGMN%7ly|?:o.g-B#0r&-CzG؍T}p/JJj]!qnmJucy8iJk&ipNI徱hTf|)oϟ Ǔr|Xa-Sth 5U;9{:gDKCӱ8Ĭ~_:ҮKƣ/td#ߣ~KtuV;B! :6,DuR/ ̩<2VyFbd,jk,lcŲc&&db-oQjr48hh n*0Pfohc:ƧM0qugLt#쐳b7Lg4<Ƨp?#dë[ELc[»~ߚWL:Z0юDOY:}v-i2[SՒB`Wn6x0~vqcRHTuyB%gUBASߥ~^S3(Ѯlϐ3ؖFrSރc5kI`)h2%ypR\ fyC3ʻςnq-w٣AZ5F gѩ`&y_-/NϹCe'JU#N{9ևa0h:>0WSK詈hP)#FVosF>/s?T8ǟh~A̘40},yεKKEk/!OX5|7NG>tY0ιaacyK񩽊8㦮`ݵ::dmftP}Rwc$z2)olm0-VZ[YiFl!-K$|MؑՏu.՜MNRuo4:__ ()c!2엻x3Oq74F3cGTfm!;HZ$a41Ct0ȎS];AV~^&q[֡c\)jv Wouldn't y'know it, a big virus attack right when I have no access to the net! Sorry about all the crap that came over moby-guts last week! I've just set it to subscriber-only postings, so that should solve the problem. If you have problems with your commits not getting posted to the list please let me know. It does mean, I believe, that you will need to subscribe to the -guts list in order for your commit logs to be posted... Developers, if you haven't done so, please do! Cheers! Mark -- Mark Wilkinson, Assistant Professor (Bioinformatics) Dept. of Medical Genetics, University of British Columbia James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research 166 - 1081 Burrard St., Vancouver, BC, Canada, V6Z 1Y6 ------------------------------------------------------------------------ It just goes to show you that SOAP::Lite is more intuitive than you might think, if you know enough Perl and have the patience to dive into the source code. -Byrne Reese -http://builder.com.com/5100-6389_14-1045078-2.html ------------------------------------------------------------------------ From senger at ebi.ac.uk Wed Feb 11 19:08:23 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 12 Feb 2004 00:08:23 +0000 (GMT) Subject: [MOBY-dev] case-sensitivity In-Reply-To: <1068411475.1706.23.camel@localhost.localdomain> Message-ID: Mark, Today Rebecca pointed me out that there are problems with the Moby Graphs. And, indeed, there are. Not only for her Moby server - but also for the main Moby server. I am looking into it now - but the first thing which seems to be obviously wrong (they may be others) is about case-sensitivity of entity names. I will tell you what I see and you wil tell me if it is normal, strange or wrong. Let's talk about data types (I assume that the same can be seen by other entities as well but I have not checked): If I ask for all data types names ('retrieveObjectNames') I am getting (for example for a string data type): So far, so good. If I ask for its definition ('retrieveObjectDefinition') I am getting: urn:lsid:biomoby.org:objectclass:String .... Which seems okay because both methods returned 'String' (one as the whole name, the second one as a last part of an LSID). But if I do the same thing with the Rebecca's server, I get first 'String' but the 'retrieveObjectDefinition' returns: urn:lsid:biomoby.org:objectclass:string Notice that now the last part of the LSID is 'string' with lower-case. The LSID specification explicitly says that starting from the 'namespace' field it is case-sensitive. However, perhaps BioMoby does not care and treats LSID as case-insensitive (meaning actually that it recognizes the same object under many different LSIDs - differing by the cases). Is this the case? Or does Rebecca's server do something wrong? When this is answered and discussed I will look further why graphs are not being created properly... Thanks, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Wed Feb 11 17:20:28 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 11 Feb 2004 16:20:28 -0600 Subject: [MOBY] [MOBY-dev] case-sensitivity In-Reply-To: References: Message-ID: <1076538028.1677.134.camel@localilluminae.com> Hi all, It is likely that Rebecca needs to update her database. As soon as Sean M. gave me assurances that the bug in the LSID stack that forced lower-case ID's had been fixed, I then went into the database by hand and changed all of the entries such that the LSID and the Objectname had the same case (as you and others had requested). This is how it was meant to be in the first place, but the bug had mucked things up such that the LSID's all had to be lower case regardless of the case of the original name of the Object (or service, or namespace). M On Wed, 2004-02-11 at 18:08, Martin Senger wrote: > Mark, > Today Rebecca pointed me out that there are problems with the Moby > Graphs. And, indeed, there are. Not only for her Moby server - but also > for the main Moby server. > I am looking into it now - but the first thing which seems to be > obviously wrong (they may be others) is about case-sensitivity of entity > names. I will tell you what I see and you wil tell me if it is normal, > strange or wrong. > Let's talk about data types (I assume that the same can be seen by > other entities as well but I have not checked): > If I ask for all data types names ('retrieveObjectNames') I am getting > (for example for a string data type): > > > > > > So far, so good. > If I ask for its definition ('retrieveObjectDefinition') I am getting: > > > urn:lsid:biomoby.org:objectclass:String > > .... > > > Which seems okay because both methods returned 'String' (one as the > whole name, the second one as a last part of an LSID). But if I do the > same thing with the Rebecca's server, I get first 'String' but the > 'retrieveObjectDefinition' returns: > > urn:lsid:biomoby.org:objectclass:string > > Notice that now the last part of the LSID is 'string' with lower-case. > > The LSID specification explicitly says that starting from the > 'namespace' field it is case-sensitive. However, perhaps BioMoby does not > care and treats LSID as case-insensitive (meaning actually that it > recognizes the same object under many different LSIDs - differing by the > cases). Is this the case? Or does Rebecca's server do something wrong? > > When this is answered and discussed I will look further why graphs are > not being created properly... > > Thanks, > Martin -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Wed Feb 11 19:31:21 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 12 Feb 2004 00:31:21 +0000 (GMT) Subject: [MOBY] [MOBY-dev] case-sensitivity In-Reply-To: <1076538028.1677.134.camel@localilluminae.com> Message-ID: > This is how it was meant to be in the first place... > I am happy with this answer - what you said what exactly what I hope for :-) Rebecca, there may still be some other problems with graphs - I will investigate further, but perhaps you may try again after you update your database... (and let me know please) Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Wed Feb 11 17:55:06 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 11 Feb 2004 16:55:06 -0600 Subject: [MOBY] [MOBY-dev] case-sensitivity In-Reply-To: References: Message-ID: <1076540106.1677.149.camel@localilluminae.com> Ughh.... Rebecca is going to KILL me next week in Madrid! She HATES it when I give her more work to do! ;-) M On Wed, 2004-02-11 at 18:31, Martin Senger wrote: > > This is how it was meant to be in the first place... > > > I am happy with this answer - what you said what exactly what I hope > for :-) > Rebecca, there may still be some other problems with graphs - I will > investigate further, but perhaps you may try again after you update your > database... (and let me know please) > > Martin -- Mark Wilkinson Illuminae From lstein at cshl.edu Fri Feb 13 10:57:37 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri, 13 Feb 2004 17:57:37 +0200 Subject: [MOBY-dev] Fwd: [MOBY-l] Proposed dates for MOBY meeting Message-ID: <200402131757.37271.lstein@cshl.edu> -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From markw at illuminae.com Fri Feb 13 11:55:14 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 13 Feb 2004 10:55:14 -0600 Subject: [MOBY-dev] [Fwd: Re: [MOBY] Re: [MOBY-l] Proposed dates for MOBY meeting] Message-ID: <1076691314.2024.16.camel@localilluminae.com> flipping this conversation over to the correct list... Hi Lincoln! Thanks for the invitation! I could probably swing it for April as well. The earlier dates are much better for me also. Mark On Fri, 2004-02-13 at 10:21, Martin Senger wrote: > > On Fri, 2004-02-13 at 10:21, Lincoln Stein wrote: > > How about the weekends of April 3-4 or April 10-11 for the next MOBY > > meeting? > > > 3-4 April much better, because April 9-12 are Easter Holidays > Martin -- Mark Wilkinson Illuminae From lstein at cshl.edu Mon Feb 16 04:47:39 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 16 Feb 2004 11:47:39 +0200 Subject: [MOBY-dev] Re: [MOBY-l] Proposed dates for MOBY meeting In-Reply-To: <1509.200.71.12.137.1076794531.squirrel@uhura.sdsc.edu> References: <200402131733.08070.lstein@cshl.edu> <1509.200.71.12.137.1076794531.squirrel@uhura.sdsc.edu> Message-ID: <200402161147.39223.lstein@cshl.edu> OK, it looks like we're on for the April 3-4 dates. Please send me a list of the number of people from your group who will be attending and I will make the arrangements. Lincoln On Saturday 14 February 2004 11:35 pm, steube at sdsc.edu wrote: > Hi all from Montevideo, Uruguay. I gave a MOBY presentation earlier > this week and next another next week. > > Apr 3, 4 sounds good to me and Gribskov can probably attend, too. > > Ken > > > Hi, > > > > How about the weekends of April 3-4 or April 10-11 for the next > > MOBY meeting? I would be happy to host it at CSHL. Before that > > I'm pretty busy with various meetings, and after that Gary is > > traveling. > > > > Lincoln > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > _______________________________________________ > > moby-l mailing list > > moby-l at biomoby.org > > http://biomoby.org/mailman/listinfo/moby-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From mycampaign at bmesrv2.com Tue Feb 17 23:28:20 2004 From: mycampaign at bmesrv2.com (=?iso-8859-1?Q?TrimGen_Genetic_Technology-_New_Mutation_Detection_Technology?=) Date: Tue, 17 Feb 2004 23:28:20 -0500 Subject: [MOBY-dev] New Mutation Detection Technology- Faster and More Accurate than Sequencing Message-ID: <200402180603.i1I63f9Q006210@portal.open-bio.org> Dear Researcher, Hello from TrimGen Genetic Technology. We want to take this time to tell you about our new?mutation detection kit called Mutector?, and?give you a special?offer on your first kit?to see the difference that TrimGen?and the Mutector? technology makes. ?? Product Spotlight Mutector? is designed to identify the mutant base from a mixed clinical sample, without the need of special equipment such as a sequencer. 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Powered by Benchmarkemail http://www.benchmarkemail.com REPORT ABUSE http://www.benchmarkemail.com/link/report_abuse.asp?   From markw at illuminae.com Thu Feb 19 01:20:50 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 18 Feb 2004 22:20:50 -0800 Subject: [MOBY-dev] Uruguay hits the webstats :-) Message-ID: <1077171650.2062.30.camel@localilluminae.com> Hey Ken et al. Uruguay is now a peculiar blip in the web stats for MOBY Central :-) http://mobycentral.cbr.nrc.ca/AccessLog.html#dom the Canadian accesses are primarily the moby client talking to moby central. The German/Spanish/UK accesses are probably (??) mostly the PlaNet consortium, with the notable exception of Martin's accesses from ebi. Then there is Uruguay - a funny little blip on the map! It made me chuckle :-) Interesting stats, though... e.g. >10,000 requests from PlaNet(?) in just 49 days... and that is an underestimate since they have their own MOBY Central installed at MIPS. Heiko/Rebecca - does your embedded client make *any* of its calls to the public registry, or are they all to your own? Do you have any embedded calls to any of my services running from MOBY Central? I'm just trying to understand whether the European calls are coming primarily from you, or if there is another group(s) using MOBY heavily over there that I am not aware of...?? Another interesting bit of information in there is farther down the page http://mobycentral.cbr.nrc.ca/AccessLog.html#req We will be able to track which objects are most often used, since the ontology server makes calls to retrieve the LSID for the various object types, and this shows up in the GET string :-) Mark -- Mark Wilkinson, Assistant Professor (Bioinformatics) Dept. of Medical Genetics, University of British Columbia James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research 166 - 1081 Burrard St. Vancouver, BC, Canada, V6Z 1Y6 tel: (604) 806 2129 fax: (604) 806 9274 ------------------------------------------------------------------------ It just goes to show you that SOAP::Lite is more intuitive than you might think, if you know enough Perl and have the patience to dive into the source code. -Byrne Reese -http://builder.com.com/5100-6389_14-1045078-2.html ------------------------------------------------------------------------ From markw at illuminae.com Mon Feb 23 16:35:55 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 23 Feb 2004 13:35:55 -0800 Subject: [MOBY-dev] whitespace in MOBY Objects Message-ID: <1077572155.1643.107.camel@localilluminae.com> Dave Waddell pointed out to me last week that the output from some of my services doesn't parse "nicely" - in particular, when I am passing back e.g. a genbank flat file, along with cross-references, the XML parsers may (in some Perl parsers this is a switchable option) interpret newlines and tabs as whitespace. Thus my output: genbank flatfile here _______ _______ _______ _______ is actually parsed to the following string: " genbank flatfile here _________ _________ _________ _________ " which is obviously not a valid genbank file format! I have just updated my services to be less cavalier about whitespace, but we should probably all look at our services and do the same. This is only important w.r.t. objects that inherit from one of the primitives (String, Integer, etc), since other objects by definition are NOT allowed to have literal content, but it is probably good practice to not be thinking about human readability when constructing our output. I will probably migrate all of my services to use an XML-DOM builder, rather than writing out the XML by hand in the future to ensure that I don't do this by accident. Thanks for the heads-up Dave! Mark -- Mark Wilkinson Illuminae From markw at illuminae.com Wed Feb 25 20:16:33 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 25 Feb 2004 17:16:33 -0800 Subject: [MOBY-dev] Acknowledging MOBY-S in your code and on your pages Message-ID: <1077758193.1916.43.camel@localilluminae.com> Hi all, In an effort to get a more accurate measure of "impact" for the granting agencies, I have made a "powered by" icon. I would greatly appreciate it if anyone who is building web pages that include content derived by calls to MOBY Central or MOBY Services could link to this icon so that I can measure hits/distribution. http://www.biomoby.org/link_to_us.html Thanks a lot everyone! Mark -- Mark Wilkinson, Assistant Professor (Bioinformatics) Dept. of Medical Genetics, University of British Columbia James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research 166 - 1081 Burrard St. Vancouver, BC, Canada, V6Z 1Y6 tel: (604) 682 2344 ext. 62129 fax: (604) 806 9274 ------------------------------------------------------------------------ It just goes to show you that SOAP::Lite is more intuitive than you might think, if you know enough Perl and have the patience to dive into the source code. -Byrne Reese -http://builder.com.com/5100-6389_14-1045078-2.html ------------------------------------------------------------------------ From lstein at cshl.edu Fri Feb 27 10:40:49 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri, 27 Feb 2004 17:40:49 +0200 Subject: [MOBY-dev] April 3-4 meeting In-Reply-To: <1077758193.1916.43.camel@localilluminae.com> References: <1077758193.1916.43.camel@localilluminae.com> Message-ID: <200402271740.49773.lstein@cshl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I am waiting for CSHL to get back to me on the availability of housing and rooms, but should know early next week whether I can confirm the April 3-4 dates. Lincoln - -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) iD8DBQFAP2UB0CIvUP7P+AkRAoN3AJ0TkJBdreyQX4wH6PvlGiUVoX+CSACfb180 gbFv0o1B6DxN8GHZVLqr5dY= =ZEuI -----END PGP SIGNATURE----- From lstein at cshl.edu Fri Feb 27 10:40:49 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri, 27 Feb 2004 17:40:49 +0200 Subject: [MOBY-dev] April 3-4 meeting In-Reply-To: <1077758193.1916.43.camel@localilluminae.com> References: <1077758193.1916.43.camel@localilluminae.com> Message-ID: <200402271740.49773.lstein@cshl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I am waiting for CSHL to get back to me on the availability of housing and rooms, but should know early next week whether I can confirm the April 3-4 dates. Lincoln - -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) iD8DBQFAP2UB0CIvUP7P+AkRAoN3AJ0TkJBdreyQX4wH6PvlGiUVoX+CSACfb180 gbFv0o1B6DxN8GHZVLqr5dY= =ZEuI -----END PGP SIGNATURE----- From markw at illuminae.com Fri Feb 27 19:00:22 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 27 Feb 2004 16:00:22 -0800 Subject: [MOBY-dev] For those interested in RDF Message-ID: <1077926422.1910.110.camel@localilluminae.com> Hi all, http://biomoby.org/cgi-bin/RESOURCES/MOBY-S/FULL I've just finished putting together version 2 of the RDF graph of MOBY Central. This should make the "purists" a bit happier since the resources in this graph actually point to other RDF graphs (rather than being LSID's as they were in the first version), and more importantly I am only using my own predicates when I absolutely have to. I still haven't found a way of representing the HAS* relationships using traditional RDF predicates, so anyone who wants to send some suggestions to the list in this regard is more than welcome. All graphs are auto-generated from the RESOURCES script, so they should be up-to-date with the registry at all times. Damian, what would I need to add to this in order for you to query it in a useful way? Does this bring us any closer to "grand unification" or are we still worlds apart? w.r.t. MOBY Objects - I've written a few quick n dirty scripts that convince me that it should be possible to (easily!) auto-convert instantiated MOBY Objects into an equivalent RDF representation... it occurred to me while writing these that MOBY Objects ~fulfil the failed promise of XML - that it should be self-describing data. The MOBY-S object structure is so tightly intertwined with the ontology that representing objects is as easy as generating the RDF graph of the ontology itself! Anyway, if this is true, this might also help in bridging the gap between MOBYShMOBY... Anyway, just random thoughts on a Friday afternoon. I go beer now. Any comments on the RDF are welcome! especially if you find errors (logical or technical). Have a great weekend everyone! Mark -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From bichnguyen at Att.net Sun Feb 29 18:22:23 2004 From: bichnguyen at Att.net (bichnguyen@Att.net) Date: Sun, 29 Feb 2004 18:22:23 -0500 Subject: [MOBY-dev] Registration confirmation Message-ID: Subj From postmaster at diplobel.org Mon Feb 2 10:42:52 2004 From: postmaster at diplobel.org (System Administrator) Date: Mon, 2 Feb 2004 05:42:52 -0500 Subject: [MOBY-dev] Undeliverable: hello Message-ID: <8A1A6B6EE755D411ADB20050041783100249708E@PHOEBE> Your message To: adam at diplobel.org Subject: hello Sent: Mon, 2 Feb 2004 05:46:34 -0500 did not reach the following recipient(s): adam at diplobel.org on Mon, 2 Feb 2004 05:42:50 -0500 The recipient name is not recognized The MTS-ID of the original message is: c=us;a= ;p=diplobel;l=PHOEBE0402021042D0G4JNVC MSEXCH:IMS:Diplobel:DIPLOBEL:PHOEBE 0 (000C05A6) Unknown Recipient From bdfy at hotmail.com Tue Feb 3 00:10:15 2004 From: bdfy at hotmail.com (bdfy at hotmail.com) Date: Tue, 3 Feb 2004 01:10:15 +0100 Subject: [MOBY-dev] Hi Message-ID: <200402030016.i130GSEs029932@portal.open-bio.org> From postmaster at diplobel.org Tue Feb 3 00:06:58 2004 From: postmaster at diplobel.org (System Administrator) Date: Mon, 2 Feb 2004 19:06:58 -0500 Subject: [MOBY-dev] Undeliverable: hi Message-ID: <8A1A6B6EE755D411ADB200500417831002515F8A@PHOEBE> Your message To: adam at diplobel.org Subject: hi Sent: Mon, 2 Feb 2004 19:10:49 -0500 did not reach the following recipient(s): adam at diplobel.org on Mon, 2 Feb 2004 19:06:54 -0500 The recipient name is not recognized The MTS-ID of the original message is: c=us;a= ;p=diplobel;l=PHOEBE04020300061FMDK4S3 MSEXCH:IMS:Diplobel:DIPLOBEL:PHOEBE 0 (000C05A6) Unknown Recipient From postmaster at diplobel.org Tue Feb 3 09:50:14 2004 From: postmaster at diplobel.org (System Administrator) Date: Tue, 3 Feb 2004 04:50:14 -0500 Subject: [MOBY-dev] Undeliverable: Error Message-ID: <8A1A6B6EE755D411ADB200500417831002507A05@PHOEBE> Your message To: steve at diplobel.org Subject: Error Sent: Tue, 3 Feb 2004 04:54:01 -0500 did not reach the following recipient(s): steve at diplobel.org on Tue, 3 Feb 2004 04:50:09 -0500 The recipient name is not recognized The MTS-ID of the original message is: c=us;a= ;p=diplobel;l=PHOEBE04020309501FMDK7KB MSEXCH:IMS:Diplobel:DIPLOBEL:PHOEBE 0 (000C05A6) Unknown Recipient From MAILER-DAEMON at mail1.chek.com Fri Feb 6 13:12:10 2004 From: MAILER-DAEMON at mail1.chek.com (MAILER-DAEMON at mail1.chek.com) Date: 6 Feb 2004 13:12:10 -0000 Subject: [MOBY-dev] failure notice Message-ID: <200402061318.i16DIDHH017661@portal.open-bio.org> Hi. This is the qmail-send program at mail1.chek.com. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : User's Disk Quota Exceeded. Sorry, your message cannot be delivered as the recipient has exceeded their disk space limit for email. --- Below this line is a copy of the message. Return-Path: Received: (qmail 32631 invoked by uid 0); 6 Feb 2004 13:12:08 -0000 Received: from 212.68.223.9.brutele.be (HELO biomoby.org) (212.68.223.9) by maude.synacor.com with SMTP; 6 Feb 2004 13:12:08 -0000 From: moby-dev at biomoby.org To: jimmy at freeze.com Subject: Mail Transaction Failed Date: Fri, 6 Feb 2004 14:12:22 +0100 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0013_FA914C66.354BE840" X-Priority: 3 X-MSMail-Priority: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0013_FA914C66.354BE840 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit ???Ea {A0? d??{??[?|??1-?v???*N??E?b?"???c'??2R(??wA??b&????$?? ?((2F?*? uA???Hq?Le?r????M??\D ???"??N????m?;$?^?1?C????R???Z??r??????]??{???????????????t??Zkit???}Z%I??\?m|!b???LO^?|S????????U??(??Mj8?-???2"?.?T??xTmS#T??T???-v0;????(????Wij? ?LhEU2/??2??dW???????_??]???g]??9dF?d???8??v1?dIxW?h??b%??K???2i?&???qNS???E?2?????xC??V?d?????3` \?;????O??????$???w?xk?m{??pa][???W????0lHuj'w??L??lD????[????n1???ZO?n??8i!?LK??N#3?m???r?????????S?|??FU?|#?]4NFK??&W?6;??l?p?V????9>?W5-?H????b????'f?K_????????i??-?????t??y?q?i?8?fEO_E?q'}??S5-N97)y) ?7???M?#?Ry?'?????ZM??GM?N%??7ly|???????:???o??.?g??-B??#?0?r???&?-CzG???T?}p/?JJj]!?qn??????mJu?c???y?8??iJ??k??&?ip?NI????h???T?f|?)o?? ????r|Xa-S?t?h ??5U;9{???:g??D?KC???8?????~_:???K????/?td???#????~??K????tuV;??B!? ?:??6??,D?u?R/???? ????0???????WS?K???????hP)#FV?osF??>?/???s????T??8???h~A???4??0},?y????K?KE??k?/???!O??X?5??|???7??N??G?>t???Y0???a??ac?y??K????8??????`????::dmft?P}??Rwc$?z2?????)??o????l??m?0?-?V?Z???[YiFl!-K?$?|??M????u?.???MNRu??o4?:?_?_?? (?)??c!2?????x????3??Oq74?F?????3cG???Tf??m!?????;HZ$??a?41Ct0???S???]???;A?V~^&???q?[????c\)??j????v? Wouldn't y'know it, a big virus attack right when I have no access to the net! Sorry about all the crap that came over moby-guts last week! I've just set it to subscriber-only postings, so that should solve the problem. If you have problems with your commits not getting posted to the list please let me know. It does mean, I believe, that you will need to subscribe to the -guts list in order for your commit logs to be posted... Developers, if you haven't done so, please do! Cheers! Mark -- Mark Wilkinson, Assistant Professor (Bioinformatics) Dept. of Medical Genetics, University of British Columbia James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research 166 - 1081 Burrard St., Vancouver, BC, Canada, V6Z 1Y6 ------------------------------------------------------------------------ It just goes to show you that SOAP::Lite is more intuitive than you might think, if you know enough Perl and have the patience to dive into the source code. -Byrne Reese -http://builder.com.com/5100-6389_14-1045078-2.html ------------------------------------------------------------------------ From senger at ebi.ac.uk Thu Feb 12 00:08:23 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 12 Feb 2004 00:08:23 +0000 (GMT) Subject: [MOBY-dev] case-sensitivity In-Reply-To: <1068411475.1706.23.camel@localhost.localdomain> Message-ID: Mark, Today Rebecca pointed me out that there are problems with the Moby Graphs. And, indeed, there are. Not only for her Moby server - but also for the main Moby server. I am looking into it now - but the first thing which seems to be obviously wrong (they may be others) is about case-sensitivity of entity names. I will tell you what I see and you wil tell me if it is normal, strange or wrong. Let's talk about data types (I assume that the same can be seen by other entities as well but I have not checked): If I ask for all data types names ('retrieveObjectNames') I am getting (for example for a string data type): So far, so good. If I ask for its definition ('retrieveObjectDefinition') I am getting: urn:lsid:biomoby.org:objectclass:String .... Which seems okay because both methods returned 'String' (one as the whole name, the second one as a last part of an LSID). But if I do the same thing with the Rebecca's server, I get first 'String' but the 'retrieveObjectDefinition' returns: urn:lsid:biomoby.org:objectclass:string Notice that now the last part of the LSID is 'string' with lower-case. The LSID specification explicitly says that starting from the 'namespace' field it is case-sensitive. However, perhaps BioMoby does not care and treats LSID as case-insensitive (meaning actually that it recognizes the same object under many different LSIDs - differing by the cases). Is this the case? Or does Rebecca's server do something wrong? When this is answered and discussed I will look further why graphs are not being created properly... Thanks, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Wed Feb 11 22:20:28 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 11 Feb 2004 16:20:28 -0600 Subject: [MOBY] [MOBY-dev] case-sensitivity In-Reply-To: References: Message-ID: <1076538028.1677.134.camel@localilluminae.com> Hi all, It is likely that Rebecca needs to update her database. As soon as Sean M. gave me assurances that the bug in the LSID stack that forced lower-case ID's had been fixed, I then went into the database by hand and changed all of the entries such that the LSID and the Objectname had the same case (as you and others had requested). This is how it was meant to be in the first place, but the bug had mucked things up such that the LSID's all had to be lower case regardless of the case of the original name of the Object (or service, or namespace). M On Wed, 2004-02-11 at 18:08, Martin Senger wrote: > Mark, > Today Rebecca pointed me out that there are problems with the Moby > Graphs. And, indeed, there are. Not only for her Moby server - but also > for the main Moby server. > I am looking into it now - but the first thing which seems to be > obviously wrong (they may be others) is about case-sensitivity of entity > names. I will tell you what I see and you wil tell me if it is normal, > strange or wrong. > Let's talk about data types (I assume that the same can be seen by > other entities as well but I have not checked): > If I ask for all data types names ('retrieveObjectNames') I am getting > (for example for a string data type): > > > > > > So far, so good. > If I ask for its definition ('retrieveObjectDefinition') I am getting: > > > urn:lsid:biomoby.org:objectclass:String > > .... > > > Which seems okay because both methods returned 'String' (one as the > whole name, the second one as a last part of an LSID). But if I do the > same thing with the Rebecca's server, I get first 'String' but the > 'retrieveObjectDefinition' returns: > > urn:lsid:biomoby.org:objectclass:string > > Notice that now the last part of the LSID is 'string' with lower-case. > > The LSID specification explicitly says that starting from the > 'namespace' field it is case-sensitive. However, perhaps BioMoby does not > care and treats LSID as case-insensitive (meaning actually that it > recognizes the same object under many different LSIDs - differing by the > cases). Is this the case? Or does Rebecca's server do something wrong? > > When this is answered and discussed I will look further why graphs are > not being created properly... > > Thanks, > Martin -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Thu Feb 12 00:31:21 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 12 Feb 2004 00:31:21 +0000 (GMT) Subject: [MOBY] [MOBY-dev] case-sensitivity In-Reply-To: <1076538028.1677.134.camel@localilluminae.com> Message-ID: > This is how it was meant to be in the first place... > I am happy with this answer - what you said what exactly what I hope for :-) Rebecca, there may still be some other problems with graphs - I will investigate further, but perhaps you may try again after you update your database... (and let me know please) Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Wed Feb 11 22:55:06 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 11 Feb 2004 16:55:06 -0600 Subject: [MOBY] [MOBY-dev] case-sensitivity In-Reply-To: References: Message-ID: <1076540106.1677.149.camel@localilluminae.com> Ughh.... Rebecca is going to KILL me next week in Madrid! She HATES it when I give her more work to do! ;-) M On Wed, 2004-02-11 at 18:31, Martin Senger wrote: > > This is how it was meant to be in the first place... > > > I am happy with this answer - what you said what exactly what I hope > for :-) > Rebecca, there may still be some other problems with graphs - I will > investigate further, but perhaps you may try again after you update your > database... (and let me know please) > > Martin -- Mark Wilkinson Illuminae From lstein at cshl.edu Fri Feb 13 15:57:37 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri, 13 Feb 2004 17:57:37 +0200 Subject: [MOBY-dev] Fwd: [MOBY-l] Proposed dates for MOBY meeting Message-ID: <200402131757.37271.lstein@cshl.edu> -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From markw at illuminae.com Fri Feb 13 16:55:14 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 13 Feb 2004 10:55:14 -0600 Subject: [MOBY-dev] [Fwd: Re: [MOBY] Re: [MOBY-l] Proposed dates for MOBY meeting] Message-ID: <1076691314.2024.16.camel@localilluminae.com> flipping this conversation over to the correct list... Hi Lincoln! Thanks for the invitation! I could probably swing it for April as well. The earlier dates are much better for me also. Mark On Fri, 2004-02-13 at 10:21, Martin Senger wrote: > > On Fri, 2004-02-13 at 10:21, Lincoln Stein wrote: > > How about the weekends of April 3-4 or April 10-11 for the next MOBY > > meeting? > > > 3-4 April much better, because April 9-12 are Easter Holidays > Martin -- Mark Wilkinson Illuminae From lstein at cshl.edu Mon Feb 16 09:47:39 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 16 Feb 2004 11:47:39 +0200 Subject: [MOBY-dev] Re: [MOBY-l] Proposed dates for MOBY meeting In-Reply-To: <1509.200.71.12.137.1076794531.squirrel@uhura.sdsc.edu> References: <200402131733.08070.lstein@cshl.edu> <1509.200.71.12.137.1076794531.squirrel@uhura.sdsc.edu> Message-ID: <200402161147.39223.lstein@cshl.edu> OK, it looks like we're on for the April 3-4 dates. Please send me a list of the number of people from your group who will be attending and I will make the arrangements. Lincoln On Saturday 14 February 2004 11:35 pm, steube at sdsc.edu wrote: > Hi all from Montevideo, Uruguay. I gave a MOBY presentation earlier > this week and next another next week. > > Apr 3, 4 sounds good to me and Gribskov can probably attend, too. > > Ken > > > Hi, > > > > How about the weekends of April 3-4 or April 10-11 for the next > > MOBY meeting? I would be happy to host it at CSHL. Before that > > I'm pretty busy with various meetings, and after that Gary is > > traveling. > > > > Lincoln > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > _______________________________________________ > > moby-l mailing list > > moby-l at biomoby.org > > http://biomoby.org/mailman/listinfo/moby-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From mycampaign at bmesrv2.com Wed Feb 18 04:28:20 2004 From: mycampaign at bmesrv2.com (=?iso-8859-1?Q?TrimGen_Genetic_Technology-_New_Mutation_Detection_Technology?=) Date: Tue, 17 Feb 2004 23:28:20 -0500 Subject: [MOBY-dev] New Mutation Detection Technology- Faster and More Accurate than Sequencing Message-ID: <200402180603.i1I63f9Q006210@portal.open-bio.org> Dear Researcher, Hello from TrimGen Genetic Technology. We want to take this time to tell you about our new?mutation detection kit called Mutector?, and?give you a special?offer on your first kit?to see the difference that TrimGen?and the Mutector? technology makes. ?? Product Spotlight Mutector? is designed to identify the mutant base from a mixed clinical sample, without the need of special equipment such as a sequencer. 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Powered by Benchmarkemail http://www.benchmarkemail.com REPORT ABUSE http://www.benchmarkemail.com/link/report_abuse.asp?   From markw at illuminae.com Thu Feb 19 06:20:50 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 18 Feb 2004 22:20:50 -0800 Subject: [MOBY-dev] Uruguay hits the webstats :-) Message-ID: <1077171650.2062.30.camel@localilluminae.com> Hey Ken et al. Uruguay is now a peculiar blip in the web stats for MOBY Central :-) http://mobycentral.cbr.nrc.ca/AccessLog.html#dom the Canadian accesses are primarily the moby client talking to moby central. The German/Spanish/UK accesses are probably (??) mostly the PlaNet consortium, with the notable exception of Martin's accesses from ebi. Then there is Uruguay - a funny little blip on the map! It made me chuckle :-) Interesting stats, though... e.g. >10,000 requests from PlaNet(?) in just 49 days... and that is an underestimate since they have their own MOBY Central installed at MIPS. Heiko/Rebecca - does your embedded client make *any* of its calls to the public registry, or are they all to your own? Do you have any embedded calls to any of my services running from MOBY Central? I'm just trying to understand whether the European calls are coming primarily from you, or if there is another group(s) using MOBY heavily over there that I am not aware of...?? Another interesting bit of information in there is farther down the page http://mobycentral.cbr.nrc.ca/AccessLog.html#req We will be able to track which objects are most often used, since the ontology server makes calls to retrieve the LSID for the various object types, and this shows up in the GET string :-) Mark -- Mark Wilkinson, Assistant Professor (Bioinformatics) Dept. of Medical Genetics, University of British Columbia James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research 166 - 1081 Burrard St. Vancouver, BC, Canada, V6Z 1Y6 tel: (604) 806 2129 fax: (604) 806 9274 ------------------------------------------------------------------------ It just goes to show you that SOAP::Lite is more intuitive than you might think, if you know enough Perl and have the patience to dive into the source code. -Byrne Reese -http://builder.com.com/5100-6389_14-1045078-2.html ------------------------------------------------------------------------ From markw at illuminae.com Mon Feb 23 21:35:55 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 23 Feb 2004 13:35:55 -0800 Subject: [MOBY-dev] whitespace in MOBY Objects Message-ID: <1077572155.1643.107.camel@localilluminae.com> Dave Waddell pointed out to me last week that the output from some of my services doesn't parse "nicely" - in particular, when I am passing back e.g. a genbank flat file, along with cross-references, the XML parsers may (in some Perl parsers this is a switchable option) interpret newlines and tabs as whitespace. Thus my output: genbank flatfile here _______ _______ _______ _______ is actually parsed to the following string: " genbank flatfile here _________ _________ _________ _________ " which is obviously not a valid genbank file format! I have just updated my services to be less cavalier about whitespace, but we should probably all look at our services and do the same. This is only important w.r.t. objects that inherit from one of the primitives (String, Integer, etc), since other objects by definition are NOT allowed to have literal content, but it is probably good practice to not be thinking about human readability when constructing our output. I will probably migrate all of my services to use an XML-DOM builder, rather than writing out the XML by hand in the future to ensure that I don't do this by accident. Thanks for the heads-up Dave! Mark -- Mark Wilkinson Illuminae From markw at illuminae.com Thu Feb 26 01:16:33 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 25 Feb 2004 17:16:33 -0800 Subject: [MOBY-dev] Acknowledging MOBY-S in your code and on your pages Message-ID: <1077758193.1916.43.camel@localilluminae.com> Hi all, In an effort to get a more accurate measure of "impact" for the granting agencies, I have made a "powered by" icon. I would greatly appreciate it if anyone who is building web pages that include content derived by calls to MOBY Central or MOBY Services could link to this icon so that I can measure hits/distribution. http://www.biomoby.org/link_to_us.html Thanks a lot everyone! Mark -- Mark Wilkinson, Assistant Professor (Bioinformatics) Dept. of Medical Genetics, University of British Columbia James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research 166 - 1081 Burrard St. Vancouver, BC, Canada, V6Z 1Y6 tel: (604) 682 2344 ext. 62129 fax: (604) 806 9274 ------------------------------------------------------------------------ It just goes to show you that SOAP::Lite is more intuitive than you might think, if you know enough Perl and have the patience to dive into the source code. -Byrne Reese -http://builder.com.com/5100-6389_14-1045078-2.html ------------------------------------------------------------------------ From lstein at cshl.edu Fri Feb 27 15:40:49 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri, 27 Feb 2004 17:40:49 +0200 Subject: [MOBY-dev] April 3-4 meeting In-Reply-To: <1077758193.1916.43.camel@localilluminae.com> References: <1077758193.1916.43.camel@localilluminae.com> Message-ID: <200402271740.49773.lstein@cshl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I am waiting for CSHL to get back to me on the availability of housing and rooms, but should know early next week whether I can confirm the April 3-4 dates. Lincoln - -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) iD8DBQFAP2UB0CIvUP7P+AkRAoN3AJ0TkJBdreyQX4wH6PvlGiUVoX+CSACfb180 gbFv0o1B6DxN8GHZVLqr5dY= =ZEuI -----END PGP SIGNATURE----- From lstein at cshl.edu Fri Feb 27 15:40:49 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri, 27 Feb 2004 17:40:49 +0200 Subject: [MOBY-dev] April 3-4 meeting In-Reply-To: <1077758193.1916.43.camel@localilluminae.com> References: <1077758193.1916.43.camel@localilluminae.com> Message-ID: <200402271740.49773.lstein@cshl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I am waiting for CSHL to get back to me on the availability of housing and rooms, but should know early next week whether I can confirm the April 3-4 dates. Lincoln - -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) iD8DBQFAP2UB0CIvUP7P+AkRAoN3AJ0TkJBdreyQX4wH6PvlGiUVoX+CSACfb180 gbFv0o1B6DxN8GHZVLqr5dY= =ZEuI -----END PGP SIGNATURE----- From markw at illuminae.com Sat Feb 28 00:00:22 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 27 Feb 2004 16:00:22 -0800 Subject: [MOBY-dev] For those interested in RDF Message-ID: <1077926422.1910.110.camel@localilluminae.com> Hi all, http://biomoby.org/cgi-bin/RESOURCES/MOBY-S/FULL I've just finished putting together version 2 of the RDF graph of MOBY Central. This should make the "purists" a bit happier since the resources in this graph actually point to other RDF graphs (rather than being LSID's as they were in the first version), and more importantly I am only using my own predicates when I absolutely have to. I still haven't found a way of representing the HAS* relationships using traditional RDF predicates, so anyone who wants to send some suggestions to the list in this regard is more than welcome. All graphs are auto-generated from the RESOURCES script, so they should be up-to-date with the registry at all times. Damian, what would I need to add to this in order for you to query it in a useful way? Does this bring us any closer to "grand unification" or are we still worlds apart? w.r.t. MOBY Objects - I've written a few quick n dirty scripts that convince me that it should be possible to (easily!) auto-convert instantiated MOBY Objects into an equivalent RDF representation... it occurred to me while writing these that MOBY Objects ~fulfil the failed promise of XML - that it should be self-describing data. The MOBY-S object structure is so tightly intertwined with the ontology that representing objects is as easy as generating the RDF graph of the ontology itself! Anyway, if this is true, this might also help in bridging the gap between MOBYShMOBY... Anyway, just random thoughts on a Friday afternoon. I go beer now. Any comments on the RDF are welcome! especially if you find errors (logical or technical). Have a great weekend everyone! Mark -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From bichnguyen at Att.net Sun Feb 29 23:22:23 2004 From: bichnguyen at Att.net (bichnguyen at Att.net) Date: Sun, 29 Feb 2004 18:22:23 -0500 Subject: [MOBY-dev] Registration confirmation Message-ID: Subj