From edgrif at sanger.ac.uk Tue May 3 09:47:43 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Tue, 3 May 2005 14:47:43 +0100 (BST) Subject: [DAS2] more updates to das2 docs In-Reply-To: References: Message-ID: All, I've made a couple of changes to the docs in the das2 sub directory... 1) I've made the protocol doc into a template style doc, this means that all the das2 docs in that directory follow the same pattern of preparation: das2_XXX_template.html --- munging by Andrews stuff --> das2_XXX.html in other words: only edit the das2_XXX_template.html docs. It also means you can now write separate xml docs for the examples in the text and have those verified and incorporated via Andrews stuff. 2) I've put some new DAS/2 response codes into das2_protocol_template.html, these directly follow the existing section on response codes as a table of codes. Please do read/mark/inwardly digest. Ed -- ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif at sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From dalke at dalkescientific.com Wed May 4 02:58:05 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Wed, 4 May 2005 00:58:05 -0600 Subject: [DAS2] hrefs and xml:base Message-ID: <4adee633f9ac4385a8757e7533fdfacc@dalkescientific.com> Do the 'href' and 'doc_href' fields obey the xml:base directive or only the "id" fields? Andrew dalke at dalkescientific.com From edgrif at sanger.ac.uk Wed May 4 04:48:01 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Wed, 4 May 2005 09:48:01 +0100 (BST) Subject: [DAS2] Re: [DAS] Hackathon 2005 In-Reply-To: References: Message-ID: Suzanna, Hi, we met at Hinxton last autumn I think. I've been doing more stuff on DAS2 with Lincoln and it may be that there are people who would like to do stuff on DAS2. I've been working away on a replacement for xace/fmap which is called zmap and would like it to use the DAS2 protocol. To this end I have someone called Roy Storey (who is on vacation at the moment) in my group who may well be interested in being part of a DAS2 hacking group. I'm copying him and also the das2 mailing list on this. As soon as Roy gets back I will talk to him about it. Ed On Wed, 20 Apr 2005, Suzanna Lewis wrote: > (sorry for multiple postings, but please do forward to > anyone else who you think might be interested) > > ------------------------------------------------------------------------ > ----------- > > Dear everyone, > > It has been a long time and we Bioinformatics devotees are overdue for > another total-immersion coding-fest (the last hackathon was held in > Singapore February 2003, more than two years ago). Apple has offered > to host us this year, and as an added bonus include free admission to > the World-Wide Developers Conference in San Francisco the prior week. > They are also looking for some people to present interesting new > developments at the WWDC, so if you have something noteworthy please > let us know. Apple is not attaching any strings, so our work need not > address Apple-specific software or hardware areas. Apple will provide > space and hardware (and access to their engineers if we'd like). > > Week 1 (June 6-10) would be spent at the WWDC. Week 2 (June 12-16) > would be in Cupertino, at Apple's headquarters. We're free to focus > on what interests us, our tentative plans include: > > 1. Bio-ontologies software > 2. High-performance computing (e.g. large scale computations, > optimization) > 3. Image analysis > 4. Documentation > 5. Anything else that may interest you > > Our plan is to organize this much as the Aspen Center for Physics > computational biology workshops were organized (for those old enough to > remember): A couple of presentations to start the day; collaboration > and coding afterwards; time for a bit of fun (does anyone else > cycle?), and discussions in the late afternoons and evenings. > > Would everyone who is interested in attending please send us a short > description of what you would like to do, and perhaps other people who > you would like to work with. There is somewhat limited space, so we > will try to prioritize groups that have a clear focus and a need to > interact. We now this is very short notice, but we hope that there > will be enough interest to make it possible. > > We are looking into additional funding support, to pay for travel > expenses, but this is still to be decided. > > Looking forward to hearing from everyone. > George, Cyrus, Steve, and Suzanna (the Bay Area locals) > > _______________________________________________ > DAS mailing list > DAS at biodas.org > http://biodas.org/mailman/listinfo/das > > > -- ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif at sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From dalke at dalkescientific.com Wed May 4 16:07:11 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Wed, 4 May 2005 14:07:11 -0600 Subject: [DAS2] das2 validator name Message-ID: Hi all, I've been working on the DAS2 validator. I'm trying to come up with a better name than "DAS2Check". The two names I've come up with so far are "Dascyllus" (a name for a type of damselfish) and "Dasypod" (the name for armadillos). The advantages are: - they have "Das" in the name :) - it's easy to get a pretty pictures for either - the phylogenetic name gives a loose tie to genomics - my test set can pull from existing sequences - I can't find any other software with either name - for "dascyllus", a friend of mine does research in damselfish phylogenies The disadvantages: - "dascyllus" sounds similar to "bacillus" - I had to ask that same friend how to pronounce "dasypod" ("da'-see-pod" and not "day-zy-pod") - a non-descriptive name requires one extra level of indirection. "DAS2Check" gives a clue as to what it does. I also came across "dasturi" which seems great given both the "DAS" and the "URI". But it means a tip or a bribe or skimming off the top. Perhaps "DasUri"? Hmm.... Since I'm having trouble, perhaps someone here has a better idea or a comment on the above ideas? Otherwise, I'm leaning towards Dasypod. Andrew dalke at dalkescientific.com From Gregg_Helt at affymetrix.com Wed May 4 16:15:23 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Wed, 4 May 2005 13:15:23 -0700 Subject: [DAS2] hrefs and xml:base Message-ID: If we want to fully adopt the xml:base standard (which I think we do), then my interpretation is that xml:base is lexically scoped and within its scope allows any attribute that requires a URI to be potentially specified as a relative URI (relative to the xml:base) instead of an absolute URI. So I would say "href", "doc_href", "id", and a number of other attributes should obey the xml:base directive(s). Note that this doesn't preclude using an absolute URI for these values, it just also allows using a relative URI. Here's a nice concise summary of xml:base : http://www.brics.dk/~amoeller/XML/common/xbase.html 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: Tuesday, May 03, 2005 11:58 PM > To: das2 at portal.open-bio.org > Subject: [DAS2] hrefs and xml:base > > Do the 'href' and 'doc_href' fields obey the xml:base > directive or only the "id" fields? > > > 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 Wed May 4 16:44:43 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Wed, 4 May 2005 13:44:43 -0700 Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? Message-ID: So we haven't had a big DAS/2 meeting since last September, and I'm feeling the need for one. I would like to propose we meet during the upcoming BOSC or ISMB conferences in Detroit (BOSC June 23-24, ISMB June 25-29). How many of us are already planning to attend one or both of these conferences? Thanks, Gregg From allenday at ucla.edu Wed May 4 17:09:05 2005 From: allenday at ucla.edu (Allen Day) Date: Wed, 4 May 2005 14:09:05 -0700 (PDT) Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? In-Reply-To: References: Message-ID: I will only be attending BOSC and the AltSplice SIG. If you'd like to meet just before or just after, that would work for me. -Allen On Wed, 4 May 2005, Helt,Gregg wrote: > So we haven't had a big DAS/2 meeting since last September, and I'm > feeling the need for one. I would like to propose we meet during the > upcoming BOSC or ISMB conferences in Detroit (BOSC June 23-24, ISMB June > 25-29). How many of us are already planning to attend one or both of > these conferences? > > Thanks, > Gregg > > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 > From dalke at dalkescientific.com Wed May 4 17:46:41 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Wed, 4 May 2005 15:46:41 -0600 Subject: [DAS2] hrefs and xml:base In-Reply-To: References: Message-ID: <8d6083fdc293785cf3646ac5ce8defc8@dalkescientific.com> Gregg: > If we want to fully adopt the xml:base standard (which I think we do), > then my interpretation is that xml:base is lexically scoped and within > its scope allows any attribute that requires a URI to be potentially > specified as a relative URI (relative to the xml:base) instead of an > absolute URI. That's what I figured, and what I did in my code. I'll edit the docs to flag which fields are expanded by xml:base. Now for part 2 of the question, in the tag will the values ever take relative URLs? Eg, suppose some server has an SVG description of how to draw the type In a related topic, the TYPES example we have says ... Is the "bg" in the XML namespace "bg" supposed to be inserted into the key name as a string? If so, how? Using universal names ( http://www.jclark.com/xml/xmlns.htm ) like "{http://www.bioperl.org/biographics/properties}height" Or is the xmlns:bg definition there in error? This is a problem for me because the parsers I use treat XML namespaces as things that only apply to tags and attributes and throw away the namespace scope. There aren't that many people using DAS nor will there be. We could just say that certain prefixes are reserved and that people may pick a unused namespace prefix as desired. Andrew dalke at dalkescientific.com From Steve_Chervitz at affymetrix.com Wed May 4 17:51:00 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Wed, 04 May 2005 16:51:00 -0500 Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? In-Reply-To: Message-ID: I'll be at both BOSC and ISMB. Meeting somewhere in between these, or during the evenings of the BOSC days would work best for me. Steve > From: Allen Day > Date: Wed, 4 May 2005 14:09:05 -0700 (PDT) > To: "Helt,Gregg" > Cc: > Subject: Re: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? > > I will only be attending BOSC and the AltSplice SIG. If you'd like to > meet just before or just after, that would work for me. > > -Allen > > On Wed, 4 May 2005, Helt,Gregg wrote: > >> So we haven't had a big DAS/2 meeting since last September, and I'm >> feeling the need for one. I would like to propose we meet during the >> upcoming BOSC or ISMB conferences in Detroit (BOSC June 23-24, ISMB June >> 25-29). How many of us are already planning to attend one or both of >> these conferences? >> >> Thanks, >> Gregg >> >> >> _______________________________________________ >> 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 Wed May 4 18:10:26 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Wed, 4 May 2005 23:10:26 +0100 Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? In-Reply-To: References: Message-ID: I'll be there (back to the native grounds for me) I arrive on the 23rd and stay for duration. -S On May 4, 2005, at 9:44 PM, Helt,Gregg wrote: > So we haven't had a big DAS/2 meeting since last September, and I'm > feeling the need for one. I would like to propose we meet during the > upcoming BOSC or ISMB conferences in Detroit (BOSC June 23-24, ISMB > June > 25-29). How many of us are already planning to attend one or both of > these conferences? > > Thanks, > Gregg > > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From dalke at dalkescientific.com Wed May 4 18:35:49 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Wed, 4 May 2005 16:35:49 -0600 Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? In-Reply-To: References: Message-ID: <568e85a31dd8baa6f2018fbc4e8fba8d@dalkescientific.com> Gregg: > I would like to propose we meet during the upcoming BOSC or ISMB > conferences in Detroit (BOSC June 23-24, ISMB June 25-29). How > many of us are already planning to attend one or both of > these conferences? I will be there. Andrew dalke at dalkescientific.com From ed_erwin at affymetrix.com Wed May 4 19:55:11 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Wed, 04 May 2005 16:55:11 -0700 Subject: [DAS2] hrefs and xml:base In-Reply-To: <8d6083fdc293785cf3646ac5ce8defc8@dalkescientific.com> References: <8d6083fdc293785cf3646ac5ce8defc8@dalkescientific.com> Message-ID: <427960DF.6090400@affymetrix.com> Andrew Dalke wrote: > > In a related topic, the TYPES example we have says > > xmlns="http://www.biodas.org/ns/das/genome/2.00" > xmlns:xlink="http://www.w3.org/1999/xlink" > xmlns:bg="http://www.bioperl.org/biographics/properties" > xmlns:das="http://www.biodas.org/ns/das/genome/2.00" > xml:base="http://www.wormbase.org/das/genome/volvox/1/type/"> > ... > > > > > > > > > Is the "bg" in the XML namespace "bg" supposed to be inserted > into the key name as a string? If so, how? Using universal > names ( http://www.jclark.com/xml/xmlns.htm ) like > "{http://www.bioperl.org/biographics/properties}height" > > Or is the xmlns:bg definition there in error? > I also wondered about this. I assumed that the "bg:" is a mistake, because later there is an example of this feature type request: http://www.wormbase.org/das/genome/volvox/1/type/tRNAscan/citation Here, ".../citation" is used, rather than ".../bg:citation", but it is my understanding that the key is supposed to literally map to the name used in constructing that type request URL. I have two other question/comments on that document ( http://biodas.org/documents/das2/das2_get.html ): > (zero or more) > indicates which representations are available for objects > within the given namespace. Does this mean *all* objects in the given namespace will be available in *all* of the given format ? or that *some* will be available in each of the listed formats ? In the example response to this query, the "sequence-ontology" header is commented-out for no good reason: http://www.wormbase.org/das/genome/volvox/1/type/tRNAscan?format=compact From lstein at cshl.edu Wed May 4 19:59:04 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Wed, 4 May 2005 19:59:04 -0400 Subject: [DAS2] hrefs and xml:base In-Reply-To: <8d6083fdc293785cf3646ac5ce8defc8@dalkescientific.com> References: <8d6083fdc293785cf3646ac5ce8defc8@dalkescientific.com> Message-ID: <200505041959.04164.lstein@cshl.edu> Hi, I think that the current spec uses xml:base in the way that the standard intends, but please feel free to insert clarifications & corrections. As far as putting the bg: prefix into the key name, it was intended to indicate that the key "glyph" belongs to the list of properties located at http://www.bioperl.org/biographics/properties. Now, I didn't find any references to tell me how to namespace an attribute value, so I just fudged things. Are there better ways to do this? Lincoln On Wednesday 04 May 2005 17:46, Andrew Dalke wrote: > Gregg: > > If we want to fully adopt the xml:base standard (which I think we do), > > then my interpretation is that xml:base is lexically scoped and within > > its scope allows any attribute that requires a URI to be potentially > > specified as a relative URI (relative to the xml:base) instead of an > > absolute URI. > > That's what I figured, and what I did in my code. > > I'll edit the docs to flag which fields are expanded by xml:base. > > Now for part 2 of the question, in the tag will > the values ever take relative URLs? Eg, suppose some > server has an SVG description of how to draw the type > > > > In a related topic, the TYPES example we have says > > xmlns="http://www.biodas.org/ns/das/genome/2.00" > xmlns:xlink="http://www.w3.org/1999/xlink" > xmlns:bg="http://www.bioperl.org/biographics/properties" > xmlns:das="http://www.biodas.org/ns/das/genome/2.00" > xml:base="http://www.wormbase.org/das/genome/volvox/1/type/"> > .. > > > > > > > > > Is the "bg" in the XML namespace "bg" supposed to be inserted > into the key name as a string? If so, how? Using universal > names ( http://www.jclark.com/xml/xmlns.htm ) like > "{http://www.bioperl.org/biographics/properties}height" > > Or is the xmlns:bg definition there in error? > > This is a problem for me because the parsers I use treat > XML namespaces as things that only apply to tags and attributes > and throw away the namespace scope. > > There aren't that many people using DAS nor will there > be. We could just say that certain prefixes are reserved > and that people may pick a unused namespace prefix as desired. > > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From lstein at cshl.edu Wed May 4 19:59:33 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Wed, 4 May 2005 19:59:33 -0400 Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? In-Reply-To: References: Message-ID: <200505041959.34065.lstein@cshl.edu> I'll be there for BOSC, but I'm not sure about ISMB, so during BOSC would be the safer bet. Lincoln On Wednesday 04 May 2005 17:51, Chervitz, Steve wrote: > I'll be at both BOSC and ISMB. Meeting somewhere in between these, or > during the evenings of the BOSC days would work best for me. > > Steve > > > From: Allen Day > > Date: Wed, 4 May 2005 14:09:05 -0700 (PDT) > > To: "Helt,Gregg" > > Cc: > > Subject: Re: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? > > > > I will only be attending BOSC and the AltSplice SIG. If you'd like to > > meet just before or just after, that would work for me. > > > > -Allen > > > > On Wed, 4 May 2005, Helt,Gregg wrote: > >> So we haven't had a big DAS/2 meeting since last September, and I'm > >> feeling the need for one. I would like to propose we meet during the > >> upcoming BOSC or ISMB conferences in Detroit (BOSC June 23-24, ISMB June > >> 25-29). How many of us are already planning to attend one or both of > >> these conferences? > >> > >> Thanks, > >> Gregg > >> > >> > >> _______________________________________________ > >> 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 Wed May 4 20:30:53 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Wed, 4 May 2005 20:30:53 -0400 Subject: [DAS2] hrefs and xml:base In-Reply-To: <427960DF.6090400@affymetrix.com> References: <8d6083fdc293785cf3646ac5ce8defc8@dalkescientific.com> <427960DF.6090400@affymetrix.com> Message-ID: <200505042030.53717.lstein@cshl.edu> On Wednesday 04 May 2005 19:55, Ed Erwin wrote: > Andrew Dalke wrote: > > In a related topic, the TYPES example we have says > > > > > xmlns="http://www.biodas.org/ns/das/genome/2.00" > > xmlns:xlink="http://www.w3.org/1999/xlink" > > xmlns:bg="http://www.bioperl.org/biographics/properties" > > xmlns:das="http://www.biodas.org/ns/das/genome/2.00" > > xml:base="http://www.wormbase.org/das/genome/volvox/1/type/"> > > ... > > > > > > > > > > > > > > > > > > Is the "bg" in the XML namespace "bg" supposed to be inserted > > into the key name as a string? If so, how? Using universal > > names ( http://www.jclark.com/xml/xmlns.htm ) like > > "{http://www.bioperl.org/biographics/properties}height" > > > > Or is the xmlns:bg definition there in error? > > I also wondered about this. > > I assumed that the "bg:" is a mistake, because later there is an example > of this feature type request: > > http://www.wormbase.org/das/genome/volvox/1/type/tRNAscan/citation > > Here, ".../citation" is used, rather than ".../bg:citation", but it is > my understanding that the key is supposed to literally map to the > name used in constructing that type request URL. > > > I have two other question/comments on that document ( > > http://biodas.org/documents/das2/das2_get.html ): > > (zero or more) > > indicates which representations are available for objects > > within the given namespace. > > Does this mean *all* objects in the given namespace will be available in > *all* of the given format ? or that *some* will be available in each of > the listed formats ? All objects in the given namespace will be available in all of the given formats. Lincoln From dalke at dalkescientific.com Thu May 5 12:42:35 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Thu, 5 May 2005 10:42:35 -0600 Subject: [DAS2] Dasypus status Message-ID: (See, I'm trying out one of the possible names) I've implemented the core architecture over the last few days. It took some head-banging, and sadly not the fun kind. The result is somewhat sweet. The difficulty was because I wanted to test the various sorts of things that could go wrong. This include: - HTTP server doesn't respond, infinite loop, etc. - the wrong values in the HTTP headers (eg, wrong version) - invalid XML returned [1] - wrong elements in the XML [2] - wrong fields in the XML [3] [1] We should add a new DAS header which is the server version. Eg, some of the DAS/1 servers returned invalid XML, like when the "&" attribute needs to be escaped. I want to allow a cleanup, triggered on the server type, that fixes these sorts of errors. [2] While the schema can catch these, some are errors while others (like extending the XML) should be warnings. [3] For example, the prototype server uses the wrong namespace and wrong xml:base. I've told Allen about it but in the meanwhile I've put a host-based cleanup filter in place. In addition several layers of the architecture are easily exchangeable with others. For example: - the "URL opener" is replaceable. This lets me put in test code to check that the URL of a request is as expected, lets me wrote a standalone proxy system to use local files for http requests, and potentially lets someone implement, say, an interface that reads directly from a MySQL connection instead of going through the web. (Hmmm, interesting ... I had just thought of that possibility.) - the "builder" layer is replaceable. This is the one that in most apps takes the input socket connection and makes a usable data structure from it. I have one builder for Python data structures. I'll soon have one for the schema checker and another that allows both builders to work. - the "build a Python data structure" knows that a few data structures are special and could be converted into something other than a string or integer. One example is the ISO date, which by default gets turned into a Python datetime. Another is a link from one part of DAS to another. By default it's a string but I experimented with a version that fetches the given link on request, which makes the data structure act like a direct mirror of the DAS object network. In doing this I noticed a couple of problems with the DAS XML we have. I've pointed out a couple. I'm in the process of cleaning up a few others. I am able to read all of the XML in the DAS CVS repository and Allen's SOURCES url. The server has been down the last few days and I haven't been able to get any further. The next steps for me are: - we were going to change the section of the spec, right? What were the changes? - check Dasypus into CVS - implements builders for the RNG validation and to let both the RNG and Python data structure builders work. - finish the error/warning handling code - clean up the example XML files - start developing test sets - work with Allen's prototype server - implement the handler for the compact formats (Again, what's the reason for the compact formats?) All that is to check that a request/response works. The next stage is to check for system integrity. I'm not close enough to that yet to describe the steps involved. Andrew dalke at dalkescientific.com From ed_erwin at affymetrix.com Thu May 5 13:26:02 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Thu, 05 May 2005 10:26:02 -0700 Subject: [DAS2] Questions on the DAS2 spec Message-ID: <427A572A.9040904@affymetrix.com> I recently re-read the document http://biodas.org/documents/das2/das2_protocol.html#overview It is looking pretty good. But there were areas that I didn't understand, and others that I want to comment on. I'll post my questions/comments one-per-email to make discussion easier. - First issue: I'd like to clear-up the requirements for the base URL. All URL examples begin something like this: http://server/das/..... Is it permissable for "server" to contain "/" characters? Is it permissable to use "https://" instead of "http://" Is it really required that the string "/das/" be part of the url? It would be useful, mainly for testing purposes, to be able to run multiple DAS2 servers on a single IP address, like this: http://netaffxdas.affymetrix.com/public/das/ https://netaffxdas.affymetrix.com/private/das/ http://netaffxdas.affymetrix.com/testing/das2/ http://netaffxdas.affymetrix.com:9091/testing/das/ Thus "server" needs to be able to include un-escaped "/" characters, and maybe even ":" for designating ports. Maybe that was already intended, but there are no such examples given in the spec. I'd rather replace all the URL examples with http(s)://urlbase/... where urlbase can contain "/" and does not necessarily have to include the string "/das/". In particular, some places that already have a DAS1 server running on "/das" may want to use "/das2" for any new server. Cheers, Ed From ed_erwin at affymetrix.com Thu May 5 13:37:59 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Thu, 05 May 2005 10:37:59 -0700 Subject: [DAS2] DAS status codes Message-ID: <427A59F7.20003@affymetrix.com> My next set of questions/comments on http://biodas.org/documents/das2/das2_protocol.html#overview are about the status codes. >> X-DAS-Status: XXX status code The spec should make a point of mentioning that the X-DAS-Status header code is NOT the same as HTTP status codes. Even when the X-DAS-Status code is 501 (indicating an error), the HTTP status code should be 200 (indicating that the DAS server actually heard and responded to the request). (This is because the HTTP status codes already have specific meanings and the software packages that the clients use to access the web may notice those codes and take unwanted actions as a result.) - Codes 201 and 205 seem redundant, or else I don't understand the distinction. - Can we consider 200,400,500 to be a generic OK/CLIENT ERROR/SERVER ERROR response when the server doesn't know how to return a more specific 2xx,4xx,5xx code? This would mean changing the definition of "400" which is currently listed as > 400 == The request could not be understood by the server due to malformed syntax. In keeping with the idea that codes ending in "00" are generic, I suggest 400 == "Bad request (not otherwise specified)." and we would need a new code for "malformed syntax". From ed_erwin at affymetrix.com Thu May 5 13:39:11 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Thu, 05 May 2005 10:39:11 -0700 Subject: [DAS2] Data Source Request Message-ID: <427A5A3F.5010805@affymetrix.com> More comments on http://biodas.org/documents/das2/das2_protocol.html#overview In the data source request, http://server/das/genome/sourceid it says > sourceid and version can be any combination of characters Hmmm, are all characters really OK? Even "/" ? Shouldn't it state "sourceid and version can contain any combination of URLEncoded characters. From ed_erwin at affymetrix.com Thu May 5 13:43:45 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Thu, 05 May 2005 10:43:45 -0700 Subject: [DAS2] Meeting Message-ID: <427A5B51.6020901@affymetrix.com> I may be a little late for the meeting this morning, but I will call in when I can. Gregg should initiate the conference call from his phone. 1-800-531-3250 id 2879055 From lstein at cshl.edu Thu May 5 15:39:12 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 5 May 2005 15:39:12 -0400 Subject: [DAS2] DAS2 phone call schedules Message-ID: <200505051539.12196.lstein@cshl.edu> Could someone send me the schedule for the calls, and the number to call in from? Thanks, Lincoln From lstein at cshl.edu Thu May 5 15:44:19 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 5 May 2005 15:44:19 -0400 Subject: [DAS2] Dasypus status In-Reply-To: References: Message-ID: <200505051544.19121.lstein@cshl.edu> > The next steps for me are: > - we were going to change the section of the > spec, right? What were the changes? I don't know! What *were* the changes? Lincoln > > - check Dasypus into CVS > > - implements builders for the RNG validation and to > let both the RNG and Python data structure builders work. > > - finish the error/warning handling code > > - clean up the example XML files > > - start developing test sets > > - work with Allen's prototype server > > - implement the handler for the compact formats > (Again, what's the reason for the compact formats?) > > All that is to check that a request/response works. > The next stage is to check for system integrity. > I'm not close enough to that yet to describe the > steps involved. > > 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 Thu May 5 16:22:35 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 5 May 2005 13:22:35 -0700 Subject: [DAS2] DAS2 phone call schedules Message-ID: Apologies, I thought I had posted that info before! DAS/2 grant weekly teleconference, Thursdays at 11:30 AM Pacific time. Conference call-in number: USA: 800-531-3250 International: 303-928-2693 Conference id: 2879055 In general in this meeting we're covering a lot of ground: implementation details and progress, spec issues, organizational stuff, etc. I'd really like to start breaking this down so that we have at least one teleconference a month that focuses on just the actual DAS/2 specification and that the principals from the different sites can all attend. Then we can focus on other topics (implementation etc.) during the other weekly meetings, which not everyone would need to attend. Best compromise time for the monthly meeting so far is 10 AM Fridays. Which is still difficult for Hinxton, so I'm open to other suggestions. 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: Thursday, May 05, 2005 12:39 PM > To: das2 at portal.open-bio.org > Subject: [DAS2] DAS2 phone call schedules > > Could someone send me the schedule for the calls, and the number to call > in > from? > > Thanks, > > Lincoln > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From lstein at cshl.edu Thu May 5 16:22:51 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 5 May 2005 16:22:51 -0400 Subject: [DAS2] das2 validator name In-Reply-To: References: Message-ID: <200505051622.51510.lstein@cshl.edu> How about "Das boot"? Lincoln On Wednesday 04 May 2005 16:07, Andrew Dalke wrote: > Hi all, > > I've been working on the DAS2 validator. I'm trying to > come up with a better name than "DAS2Check". The two > names I've come up with so far are "Dascyllus" (a name for > a type of damselfish) and "Dasypod" (the name for armadillos). > > The advantages are: > - they have "Das" in the name :) > - it's easy to get a pretty pictures for either > - the phylogenetic name gives a loose tie to genomics > - my test set can pull from existing sequences > - I can't find any other software with either name > > - for "dascyllus", a friend of mine does research > in damselfish phylogenies > > The disadvantages: > - "dascyllus" sounds similar to "bacillus" > - I had to ask that same friend how to pronounce "dasypod" > ("da'-see-pod" and not "day-zy-pod") > - a non-descriptive name requires one extra level of > indirection. "DAS2Check" gives a clue as to what it does. > > > I also came across "dasturi" which seems great given both > the "DAS" and the "URI". But it means a tip or a bribe or > skimming off the top. Perhaps "DasUri"? Hmm.... > > Since I'm having trouble, perhaps someone here has a better > idea or a comment on the above ideas? Otherwise, I'm > leaning towards Dasypod. > > 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 Thu May 5 16:30:00 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 5 May 2005 13:30:00 -0700 Subject: [DAS2] das2 validator name Message-ID: Good one, I'm changing my vote from Dasypod to Das Boot! 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: Thursday, May 05, 2005 1:23 PM > To: das2 at portal.open-bio.org > Subject: Re: [DAS2] das2 validator name > > How about "Das boot"? > > Lincoln > > On Wednesday 04 May 2005 16:07, Andrew Dalke wrote: > > Hi all, > > > > I've been working on the DAS2 validator. I'm trying to > > come up with a better name than "DAS2Check". The two > > names I've come up with so far are "Dascyllus" (a name for > > a type of damselfish) and "Dasypod" (the name for armadillos). > > > > The advantages are: > > - they have "Das" in the name :) > > - it's easy to get a pretty pictures for either > > - the phylogenetic name gives a loose tie to genomics > > - my test set can pull from existing sequences > > - I can't find any other software with either name > > > > - for "dascyllus", a friend of mine does research > > in damselfish phylogenies > > > > The disadvantages: > > - "dascyllus" sounds similar to "bacillus" > > - I had to ask that same friend how to pronounce "dasypod" > > ("da'-see-pod" and not "day-zy-pod") > > - a non-descriptive name requires one extra level of > > indirection. "DAS2Check" gives a clue as to what it does. > > > > > > I also came across "dasturi" which seems great given both > > the "DAS" and the "URI". But it means a tip or a bribe or > > skimming off the top. Perhaps "DasUri"? Hmm.... > > > > Since I'm having trouble, perhaps someone here has a better > > idea or a comment on the above ideas? Otherwise, I'm > > leaning towards Dasypod. > > > > 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 Steve_Chervitz at affymetrix.com Thu May 5 19:29:33 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Thu, 05 May 2005 16:29:33 -0700 Subject: [DAS2] das2 validator name In-Reply-To: Message-ID: I like Das Boot too (motto: ?Giving DAS a Boot?), but the armadillo symbolism is fitting since armadillos are very tough and robust, and that?s good symbolism for a validation suite. Here?s another more tenuous connection between DAS and armadillos: * Some folks connected with DAS come from Drosophila labs (Gregg, Suzi) * Drosophila embryos have genes that are expressed in a striped pattern, akin to the 9-banded armadillo (and there is a Drosophila gene called armadillo: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Grap hics&list_uids=31151 ) Steve > From: "Helt,Gregg" > Date: Thu, 5 May 2005 13:30:00 -0700 > To: Lincoln Stein , > Subject: RE: [DAS2] das2 validator name > > Good one, I'm changing my vote from Dasypod to Das Boot! > > 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: Thursday, May 05, 2005 1:23 PM >> To: das2 at portal.open-bio.org >> Subject: Re: [DAS2] das2 validator name >> >> How about "Das boot"? >> >> Lincoln >> >> On Wednesday 04 May 2005 16:07, Andrew Dalke wrote: >>> Hi all, >>> >>> I've been working on the DAS2 validator. I'm trying to >>> come up with a better name than "DAS2Check". The two >>> names I've come up with so far are "Dascyllus" (a name for >>> a type of damselfish) and "Dasypod" (the name for armadillos). >>> >>> The advantages are: >>> - they have "Das" in the name :) >>> - it's easy to get a pretty pictures for either >>> - the phylogenetic name gives a loose tie to genomics >>> - my test set can pull from existing sequences >>> - I can't find any other software with either name >>> >>> - for "dascyllus", a friend of mine does research >>> in damselfish phylogenies >>> >>> The disadvantages: >>> - "dascyllus" sounds similar to "bacillus" >>> - I had to ask that same friend how to pronounce "dasypod" >>> ("da'-see-pod" and not "day-zy-pod") >>> - a non-descriptive name requires one extra level of >>> indirection. "DAS2Check" gives a clue as to what it does. >>> >>> >>> I also came across "dasturi" which seems great given both >>> the "DAS" and the "URI". But it means a tip or a bribe or >>> skimming off the top. Perhaps "DasUri"? Hmm.... >>> >>> Since I'm having trouble, perhaps someone here has a better >>> idea or a comment on the above ideas? Otherwise, I'm >>> leaning towards Dasypod. >>> >>> 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 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From ed_erwin at affymetrix.com Thu May 5 19:35:21 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Thu, 05 May 2005 16:35:21 -0700 Subject: [DAS2] das2 validator name In-Reply-To: References: Message-ID: <427AADB9.7050807@affymetrix.com> The first name I thought of myself was "Das Boot". I even started writing an e-mail to Andrew suggesting that name, but then I decided I was being too silly so I deleted it. Americans already mispronounce the "Boot" part of "Das Boot". Now we'll be encouraging the mispronounciation of "Das" as well. I like that ! Chervitz, Steve wrote: > I like Das Boot too (motto: ?Giving DAS a Boot?), From edgrif at sanger.ac.uk Fri May 6 02:00:23 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Fri, 6 May 2005 07:00:23 +0100 (BST) Subject: [DAS2] das2 validator name In-Reply-To: References: Message-ID: Andrew, how about Dastry, as in "Dastry rides again"....sorry, couldn't resist... Ed On Wed, 4 May 2005, Andrew Dalke wrote: > Hi all, > > I've been working on the DAS2 validator. I'm trying to > come up with a better name than "DAS2Check". The two > names I've come up with so far are "Dascyllus" (a name for > a type of damselfish) and "Dasypod" (the name for armadillos). > > The advantages are: > - they have "Das" in the name :) > - it's easy to get a pretty pictures for either > - the phylogenetic name gives a loose tie to genomics > - my test set can pull from existing sequences > - I can't find any other software with either name > > - for "dascyllus", a friend of mine does research > in damselfish phylogenies > > The disadvantages: > - "dascyllus" sounds similar to "bacillus" > - I had to ask that same friend how to pronounce "dasypod" > ("da'-see-pod" and not "day-zy-pod") > - a non-descriptive name requires one extra level of > indirection. "DAS2Check" gives a clue as to what it does. > > > I also came across "dasturi" which seems great given both > the "DAS" and the "URI". But it means a tip or a bribe or > skimming off the top. Perhaps "DasUri"? Hmm.... > > Since I'm having trouble, perhaps someone here has a better > idea or a comment on the above ideas? Otherwise, I'm > leaning towards Dasypod. > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 > > > -- ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif at sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From ed_erwin at affymetrix.com Fri May 6 13:16:03 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Fri, 06 May 2005 10:16:03 -0700 Subject: [DAS2] hrefs and xml:base In-Reply-To: References: Message-ID: <427BA653.3060807@affymetrix.com> The document you cite as defining xml:base leaves me with an unanswered question. It says that this is inspired by the html tag, but doesn't say whether it works in the same complex way that html works. Namely, with this base tag: This href: href="../cages/birds.gif" resolves to: http://www.aviary.com/cages/birds.gif In other words, it doesn't simply do a String concatenation of the base and the href, but rather has to throw away the "intro.html" part and interpret the meaning of ".." This example comes from http://www.w3.org/TR/REC-html40/struct/links.html#h-12.4 Is there some more complete specification of xml:base that states whether these complicated things are allowed? Helt,Gregg wrote: > If we want to fully adopt the xml:base standard (which I think we do), > then my interpretation is that xml:base is lexically scoped and within > its scope allows any attribute that requires a URI to be potentially > specified as a relative URI (relative to the xml:base) instead of an > absolute URI. > > So I would say "href", "doc_href", "id", and a number of other > attributes should obey the xml:base directive(s). Note that this > doesn't preclude using an absolute URI for these values, it just also > allows using a relative URI. > > Here's a nice concise summary of xml:base : > http://www.brics.dk/~amoeller/XML/common/xbase.html > From dalke at dalkescientific.com Fri May 6 13:39:59 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 6 May 2005 11:39:59 -0600 Subject: [DAS2] hrefs and xml:base In-Reply-To: <427BA653.3060807@affymetrix.com> References: <427BA653.3060807@affymetrix.com> Message-ID: <25d8222dbd7d513a5bd0a2ec5ac92999@dalkescientific.com> Ed: > Is there some more complete specification of xml:base that states > whether these complicated things are allowed? They are allowed. The xml:base can be contained in another xml:base and they interact as you described. The spec is at http://www.w3.org/TR/xmlbase/ Andrew dalke at dalkescientific.com From Steve_Chervitz at affymetrix.com Fri May 6 14:25:56 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Fri, 06 May 2005 11:25:56 -0700 Subject: [DAS2] hrefs and xml:base In-Reply-To: <25d8222dbd7d513a5bd0a2ec5ac92999@dalkescientific.com> Message-ID: As far as I can tell, there is no restriction that an xml:base URI must end with a /, but that seems to be the convention. In this case, constructing relative URLs by concatenating ../ onto the xml:base URI should work. Here?s an xml:base tutorial that has a bunch of examples, in all cases xml:base specifies a directory: http://www.zvon.org/xxl/XMLBaseTutorial/Output/index.html I did find an example of an xml:base that points to a file, but it?s on a MSDN site, making it therefore highly suspect: http://msdn.microsoft.com/library/default.asp?url=/library/en-us/dnxmlnet/ht ml/xinclude.asp BTW, the W3C recommendation http://www.w3.org/TR/xmlbase/ doesn't mention the use of ../ within an XML base spec. But since it's just a URI, it is allowed. See the URI spec: http://www.gbiv.com/protocols/uri/rfc/rfc3986.html#path Steve > From: Andrew Dalke > Date: Fri, 6 May 2005 11:39:59 -0600 > To: > Subject: Re: [DAS2] hrefs and xml:base > > Ed: >> Is there some more complete specification of xml:base that states >> whether these complicated things are allowed? > > They are allowed. The xml:base can be contained in another xml:base > and they interact as you described. > > The spec is at http://www.w3.org/TR/xmlbase/ > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From ed_erwin at affymetrix.com Fri May 6 14:30:00 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Fri, 06 May 2005 11:30:00 -0700 Subject: [DAS2] hrefs and xml:base In-Reply-To: <25d8222dbd7d513a5bd0a2ec5ac92999@dalkescientific.com> References: <427BA653.3060807@affymetrix.com> <25d8222dbd7d513a5bd0a2ec5ac92999@dalkescientific.com> Message-ID: <427BB7A8.7080908@affymetrix.com> Thanks. That also clears-up another question I had asked earlier (although I can't find the e-mail where I asked it.) Anyway, the question had come-up whether the contents of the 'id' attribute should be URLEncoded inside the xml document. Based on this xmlbase spec, the answer is NO. The contents of the id attributes should be XMLEncoded when necessary, but the URLEncoding will happen during the process of converting the attribute value to a URL. "processors must encode and escape these characters to obtain a valid URI reference from the attribute value" If the XML attribute value is already URLEncoded, this process would result in double-encoding. Andrew Dalke wrote: > Ed: > >> Is there some more complete specification of xml:base that states >> whether these complicated things are allowed? > > > They are allowed. The xml:base can be contained in another xml:base > and they interact as you described. > > The spec is at http://www.w3.org/TR/xmlbase/ > > 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 Sat May 7 01:12:36 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 6 May 2005 23:12:36 -0600 Subject: [DAS2] Dasypus status In-Reply-To: <200505051544.19121.lstein@cshl.edu> References: <200505051544.19121.lstein@cshl.edu> Message-ID: <0e0b66c022685cc27fd8579a8858817d@dalkescientific.com> Me: >> - we were going to change the section of the >> spec, right? What were the changes? Lincoln: > I don't know! What *were* the changes? Here's the current spec (zero or more) A property of this feature. Properties are typed using the ptype attribute. The value of the property may indicated by a URL given by the href attribute, or may be given inline as the CDATA content of the section. ptype ? a URL describing the property type href (optional) ? a URL that provides more information about the property of this feature, can be used for database XREFs mime_type (optional) ? MIME type of the CDATA contents content_encoding (optional) ? Encoding of the CDATA contents CDATA text ? Content The proposal was to get rid of the CDATA text. That makes things less complex, at the cost of a potential extra network lookup. We can get rid of the mime_type and content_encoding fields too. We don't need to have the extra lookup. A couple days ago I was reminded of the "data" URL scheme http://www.ietf.org/rfc/rfc2397.txt That RFC gives a couple of examples: data:,A%20brief%20note is the text/plain string "A brief note" Larry is an inline image of some bearded dude, in b&w. More info about the data URI scheme (dated) http://www.mozilla.org/quality/networking/docs/aboutdata.html with on-line examples at http://www.mozilla.org/quality/networking/testing/datatests.html Cool! Safari understands it! Actually, it seems that everyone except IE understand it these days. Anyway, using a data URL scheme lets us get rid of the CDATA, content_encoding and mime_type fields of the and still let us embed small chunks of data in-line. Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Tue May 10 04:10:38 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 10 May 2005 02:10:38 -0600 Subject: [DAS2] das2 validator name In-Reply-To: <200505051622.51510.lstein@cshl.edu> References: <200505051622.51510.lstein@cshl.edu> Message-ID: After considering the options I went for my first name - Dasypus. I applied for a new sf.net project. It was accepted: dasypus.sf.net I did an initial check-in of the Python code I've been working on. There will be two parts: - "das2"; a client library - "dasypus"; the validator I've been working on the client library, trying to figure out which parts go where. Eg, I discovered today I needed to support dumping the result information so I can track down and perhaps fix XML-level errors. In other news, I've been going through the back emails and moving spec proposals over to the new bug tracking database. Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Tue May 10 04:13:32 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 10 May 2005 02:13:32 -0600 Subject: [DAS2] das2 validator name In-Reply-To: References: Message-ID: Steve: > I like Das Boot too (motto: ?Giving DAS a Boot?), Along those lines I also considered "dastard". :) Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Tue May 10 04:46:20 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 10 May 2005 02:46:20 -0600 Subject: [DAS2] hrefs and xml:base In-Reply-To: References: Message-ID: <43fc505775bc621f56f249aa179ae65f@dalkescientific.com> Steve: > As far as I can tell, there is no restriction that an xml:base URI > must end with a /, but that seems to be the convention. > In this case, constructing relative URLs by concatenating ../ onto > the xml:base URI should work. If the URI doesn't end with a '/' then the last term will almost certainly be removed as part of the join. That is xml:base = "http://www.biodas.org/some/path/foo" id = "bar" should generate xml:base = "http://www.biodas.org/some/path/bar" Except for an empty id that last term ("foo") is needless. > I did find an example of an xml:base that points to a > file, but it?s on a > MSDN site, making it therefore highly suspect: > http://msdn.microsoft.com/library/default.asp?url=/library/en-us/ > dnxmlnet/html/xinclude.asp There's no problem having xml:base point to a file. > BTW, the W3C recommendation http://www.w3.org/TR/xmlbase/ > doesn't mention the use of ../ within an XML base spec. What it does is refer people to RFC 2396 for a description of how a base and relative URI interact. See section 5.2 of that spec for details. That RFC is document format independent. The xml:base spec describes how xml:base works in an XML document. The base URI of an element is: the base URI specified by an xml:base attribute on the element, if one exists, otherwise the base URI of the element's parent element within the document or external entity, if one exists, otherwise the base URI of the document entity or external entity containing the element. That's a recursive definition, so multiple xml:bases are allowed. Once the base and relative URI's are known, they are joined as defined in RFC 2396. Though I see now it's out of date. > But since it's just a URI, it is allowed. See the URI spec: > http://www.gbiv.com/protocols/uri/rfc/rfc3986.html#path RFC 3986 obsoletes the RFC 2396 mentioned in the xml:base spec. :) Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Tue May 10 06:32:14 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 10 May 2005 04:32:14 -0600 Subject: [DAS2] imported data into bug tracker Message-ID: I've imported all of the back emails for spec changes into the bug tracker at http://bugzilla.open-bio.org/ Here's the list ID Sev Pri Plt Owner State Result Summary 1783 nor P2 All lstein at cshl.org NEW requirements for the base URL 1784 nor P2 All lstein at cshl.org NEW status codes 1785 nor P2 All dalke at dalkescientific.com NEW clarify how to escape terms in the URL 1786 nor P2 All lstein at cshl.org NEW use data: URLs to simplify the tag 1787 nor P2 All dalke at dalkescientific.com NEW remove CAPABILITIES 1788 nor P2 All lstein at cshl.org NEW use "uri" instead of "id" 1789 nor P2 All lstein at cshl.org NEW use NameValueType 1790 nor P2 All lstein at cshl.org NEW ambiguity in "att=name:value" queries 1791 nor P2 All lstein at cshl.org NEW restrict a /type response to a subset of types 1792 nor P2 All lstein at cshl.org NEW allow 'type's which aren't derived from sofa 1793 nor P2 All dalke at dalkescientific.com NEW XML examples need a version string 1794 nor P2 All lstein at cshl.org NEW s in a 1795 nor P2 All lstein at cshl.org NEW bg: namespace in Andrew dalke at dalkescientific.com From Steve_Chervitz at affymetrix.com Tue May 10 15:14:01 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Tue, 10 May 2005 12:14:01 -0700 Subject: [DAS2] imported data into bug tracker In-Reply-To: Message-ID: Thanks for importing these Andrew. Jason Stajich graciously set up the DAS area in the open-bio bugzilla database for us. I was starting to add components to it. So far, there are only two, one for general spec issues and one for issues with the GET request portion of the spec. I was planning to add components for writeback portion of the spec, but haven't done that yet. I thought it might be convenient to use this bugzilla as a one-stop-shop for tracking all DAS/2 related bugs, including client, server, and validation suite. Forcing people to use different bug trackers for client, server, validation suite, and spec issues I think would be too unwieldy. Having one place to go would be easier for submitters and developers. How do folks feel about using this bugzilla db in this way? Steve > From: Andrew Dalke > Date: Tue, 10 May 2005 04:32:14 -0600 > To: > Subject: [DAS2] imported data into bug tracker > > I've imported all of the back emails for spec changes into > the bug tracker at http://bugzilla.open-bio.org/ > > Here's the list > > ID Sev Pri Plt Owner State Result Summary > 1783 nor P2 All lstein at cshl.org NEW requirements for the base URL > > 1784 nor P2 All lstein at cshl.org NEW status codes > > 1785 nor P2 All dalke at dalkescientific.com NEW clarify how to escape > terms in the URL > > 1786 nor P2 All lstein at cshl.org NEW use data: URLs to simplify the > tag > > 1787 nor P2 All dalke at dalkescientific.com NEW remove CAPABILITIES > > 1788 nor P2 All lstein at cshl.org NEW use "uri" instead of "id" > > 1789 nor P2 All lstein at cshl.org NEW use NameValueType > > 1790 nor P2 All lstein at cshl.org NEW ambiguity in "att=name:value" > queries > > 1791 nor P2 All lstein at cshl.org NEW restrict a /type response to a > subset of types > > 1792 nor P2 All lstein at cshl.org NEW allow 'type's which aren't derived > from sofa > > 1793 nor P2 All dalke at dalkescientific.com NEW XML examples need a > version string > > 1794 nor P2 All lstein at cshl.org NEW s in a > > 1795 nor P2 All lstein at cshl.org NEW bg: namespace in > > > 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 Tue May 10 15:55:58 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 10 May 2005 13:55:58 -0600 Subject: [DAS2] imported data into bug tracker In-Reply-To: References: Message-ID: <89cf814c18c217608fec492c2097e046@dalkescientific.com> Steve: > How do folks feel about using this bugzilla db [as the central > bug report system]? Fine with me. I don't think it needs to be broken down into GET and PUT components. For a small project like this I think that's too fine grained. Andrew dalke at dalkescientific.com From allenday at ucla.edu Tue May 10 16:22:10 2005 From: allenday at ucla.edu (Allen Day) Date: Tue, 10 May 2005 13:22:10 -0700 (PDT) Subject: [DAS2] imported data into bug tracker In-Reply-To: <89cf814c18c217608fec492c2097e046@dalkescientific.com> References: <89cf814c18c217608fec492c2097e046@dalkescientific.com> Message-ID: Andrew and I are putting server bugs into the sourceforge tracker, but I'd be happy to move them over to open-bio if it's easier for people. Although I personally like SF. -Allen On Tue, 10 May 2005, Andrew Dalke wrote: > Steve: > > How do folks feel about using this bugzilla db [as the central > > bug report system]? > > Fine with me. > > I don't think it needs to be broken down into GET and PUT > components. For a small project like this I think that's > too fine grained. > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 > From ed_erwin at affymetrix.com Tue May 10 16:25:46 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Tue, 10 May 2005 13:25:46 -0700 Subject: [DAS2] imported data into bug tracker In-Reply-To: References: Message-ID: <428118CA.1070300@affymetrix.com> Chervitz, Steve wrote: > I thought it might be convenient to use this bugzilla as a one-stop-shop for > tracking all DAS/2 related bugs, including client, server, and validation > suite. Please do NOT put IGB bugs in the DAS/2 bugzilla, even though it is intended to become a DAS/2 client. I already have to keep track of 3 bug-reporting repositories for IGB and I don't need a fourth one! But thanks, Andrew, for copying our e-mails over to that bugzilla. From Steve_Chervitz at affymetrix.com Tue May 10 18:10:19 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Tue, 10 May 2005 15:10:19 -0700 Subject: [DAS2] imported data into bug tracker In-Reply-To: <428118CA.1070300@affymetrix.com> Message-ID: Ed Erwin wrote: > Chervitz, Steve wrote: >> I thought it might be convenient to use this bugzilla as a one-stop-shop for >> tracking all DAS/2 related bugs, including client, server, and validation >> suite. > > Please do NOT put IGB bugs in the DAS/2 bugzilla, even though it is > intended to become a DAS/2 client. I already have to keep track of 3 > bug-reporting repositories for IGB and I don't need a fourth one! I also believe it is best to not migrate existing bugs from the established client and server bug trackers into the open-bio bugzilla db. However, there's a decent chance that people will submit new bugs on the open-bio bugzilla pertaining to anything related to DAS. Once people start getting their hands wet with DAS/2, they may naturally gravitate to bugzilla.open-bio.org, since it is close to biodas.org (in internet space). A good solution might be to have a Bugs link on biodas.org pointing to a page that describes where to go to submit/view bugs for various parts of DAS/2 that are being developed by the grant: * Bugs for the spec -> bugzilla.open-bio.org * Bugs for the IGB client -> genoviz.sf.net (or where?) * Bugs for the gmod server -> gmod.sf.net * Bugs for the validation suite -> ?? I can look into setting up this page. Steve From dalke at dalkescientific.com Wed May 11 02:23:29 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Wed, 11 May 2005 00:23:29 -0600 Subject: [DAS2] imported data into bug tracker In-Reply-To: References: Message-ID: <5263783bfe378dbb186ebeabf70daef9@dalkescientific.com> Steve: > A good solution might be to have a Bugs link on biodas.org pointing to > a > page that describes where to go to submit/view bugs for various parts > of > DAS/2 that are being developed by the grant: > > * Bugs for the spec -> bugzilla.open-bio.org > * Bugs for the IGB client -> genoviz.sf.net (or where?) > * Bugs for the gmod server -> gmod.sf.net > * Bugs for the validation suite -> ?? > > I can look into setting up this page. I personally have no preference. I can use the SF project bug tracker for Dasypus, or DAS/2 one. I can even use all 4 different trackers. I think people will tend to use the bug tracker mentioned on the main page for a given project, which can point wherever. If there is a mixup with a bug reported in the wrong system then it's easy enough to say "closed; moved to the XYZ tracker." But I honestly think there won't be that many mixups. Andrew dalke at dalkescientific.com From edgrif at sanger.ac.uk Wed May 11 10:07:33 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Wed, 11 May 2005 15:07:33 +0100 (BST) Subject: [DAS2] hackathon and das2 In-Reply-To: References: Message-ID: All, Is there any interest in doing DAS2 stuff at the proposed biohackathon in June ? I have someone in my team, Roy Storey, who could come out to work on our client (zmap) and making it work with das2. Is anyone else interested/going to this ? If people are interested it would be good to know soon as we will need to put in travel applications etc. etc. Also, could someone add Roy (rds at sanger.ac.uk) to the das2 mailing list, thanks. cheers Ed -- ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif at sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From allenday at ucla.edu Wed May 11 15:40:55 2005 From: allenday at ucla.edu (Allen Day) Date: Wed, 11 May 2005 12:40:55 -0700 (PDT) Subject: [DAS2] hackathon and das2 In-Reply-To: References: Message-ID: I'm interested to discuss DAS/2 at the biohackathon. On Wed, 11 May 2005, Ed Griffiths wrote: > All, > > Is there any interest in doing DAS2 stuff at the proposed biohackathon in June ? > > I have someone in my team, Roy Storey, who could come out to work on our client > (zmap) and making it work with das2. Is anyone else interested/going to this ? > > If people are interested it would be good to know soon as we will need to put in > travel applications etc. etc. > > > Also, could someone add Roy (rds at sanger.ac.uk) to the das2 mailing list, thanks. > > cheers Ed > From Gregg_Helt at affymetrix.com Thu May 12 10:44:09 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 12 May 2005 07:44:09 -0700 Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? Message-ID: Based on everyone's responses, it looks like there are more of us attending BOSC than ISMB. So I'd like to propose a tentative schedule: June 22, evening -- informal meeting, whoever gets there early. Dinner? June 23, afternoon/evening -- DAS/2 grantee meeting, open only to grant collaborators (basically everyone on this list) June 24, afternoon/evening -- DAS/2 BOF, open to anyone who wants to attend Thoughts? gregg P.S. I just received notice that the DAS/2 abstract I submitted for BOSC was accepted for presentation. Hopefully that will generate interest in the BOF. > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Helt,Gregg > Sent: Wednesday, May 04, 2005 1:45 PM > To: das2 at portal.open-bio.org > Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? > > So we haven't had a big DAS/2 meeting since last September, and I'm > feeling the need for one. I would like to propose we meet during the > upcoming BOSC or ISMB conferences in Detroit (BOSC June 23-24, ISMB June > 25-29). How many of us are already planning to attend one or both of > these conferences? > > Thanks, > Gregg From Gregg_Helt at affymetrix.com Thu May 12 13:07:25 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 12 May 2005 10:07:25 -0700 Subject: [DAS2] imported data into bug tracker Message-ID: I'd also really like to keep bug tracking and feature requests for the spec separate from the client and server implementations. My main reason for this is to emphasize that the spec is entirely independent of the implementations. Too many people I talk to are already confused about the distinction. There should be one spec, but multiple implementations of DAS/2 clients and servers, and not all from the grant collaborators. To me that's an indication that we've succeeded in the primary goal of the grant which is coming up with an improved DAS/2 spec that is widely adopted by the bioinformatics community. The validation suite might be an exception to this distinction. I doubt that anyone else will reimplement this, and I think it's okay for it to be more tightly associated with the spec. gregg > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Chervitz, Steve > Sent: Tuesday, May 10, 2005 3:10 PM > To: Erwin, Ed; das2 at portal.open-bio.org > Subject: Re: [DAS2] imported data into bug tracker > > > Ed Erwin wrote: > > Chervitz, Steve wrote: > >> I thought it might be convenient to use this bugzilla as a one-stop- > shop for > >> tracking all DAS/2 related bugs, including client, server, and > validation > >> suite. > > > > Please do NOT put IGB bugs in the DAS/2 bugzilla, even though it is > > intended to become a DAS/2 client. I already have to keep track of 3 > > bug-reporting repositories for IGB and I don't need a fourth one! > > I also believe it is best to not migrate existing bugs from the > established > client and server bug trackers into the open-bio bugzilla db. > > However, there's a decent chance that people will submit new bugs on the > open-bio bugzilla pertaining to anything related to DAS. Once people start > getting their hands wet with DAS/2, they may naturally gravitate to > bugzilla.open-bio.org, since it is close to biodas.org (in internet space). > > A good solution might be to have a Bugs link on biodas.org pointing to a > page that describes where to go to submit/view bugs for various parts of > DAS/2 that are being developed by the grant: > > * Bugs for the spec -> bugzilla.open-bio.org > * Bugs for the IGB client -> genoviz.sf.net (or where?) > * Bugs for the gmod server -> gmod.sf.net > * Bugs for the validation suite -> ?? > > I can look into setting up this page. > > Steve > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From dalke at dalkescientific.com Thu May 12 13:27:33 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Thu, 12 May 2005 11:27:33 -0600 Subject: [DAS2] imported data into bug tracker In-Reply-To: References: Message-ID: <7abcba93337b0cf722a57c946ad89a0c@dalkescientific.com> Gregg: > The validation suite might be an exception to this distinction. I > doubt > that anyone else will reimplement this, and I think it's okay for it to > be more tightly associated with the spec. Except that I've broken the validation code into two components. One is a das2 Python client and the other is the validator. And people may use the das2 component without using the validator. Andrew dalke at dalkescientific.com From allenday at ucla.edu Thu May 12 13:39:53 2005 From: allenday at ucla.edu (Allen Day) Date: Thu, 12 May 2005 10:39:53 -0700 (PDT) Subject: [DAS2] imported data into bug tracker In-Reply-To: <7abcba93337b0cf722a57c946ad89a0c@dalkescientific.com> References: <7abcba93337b0cf722a57c946ad89a0c@dalkescientific.com> Message-ID: Is there a distiction made between these in CVS, i.e. are they in separate repositories? Have you considered implementing some client components in C? The reason I ask is that I'm interested in having a .so to link to so that I can use a common DAS client API from R, Java, and Perl as well. -Allen On Thu, 12 May 2005, Andrew Dalke wrote: > Gregg: > > The validation suite might be an exception to this distinction. I > > doubt > > that anyone else will reimplement this, and I think it's okay for it to > > be more tightly associated with the spec. > > Except that I've broken the validation code into two components. > One is a das2 Python client and the other is the validator. And > people may use the das2 component without using the validator. > > 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 Thu May 12 13:40:54 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 12 May 2005 10:40:54 -0700 Subject: [DAS2] imported data into bug tracker Message-ID: client++; > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Andrew Dalke > Sent: Thursday, May 12, 2005 10:28 AM > To: DAS/2 > Subject: Re: [DAS2] imported data into bug tracker > > Gregg: > > The validation suite might be an exception to this distinction. I > > doubt > > that anyone else will reimplement this, and I think it's okay for it to > > be more tightly associated with the spec. > > Except that I've broken the validation code into two components. > One is a das2 Python client and the other is the validator. And > people may use the das2 component without using the validator. > > 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 Thu May 12 13:43:46 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 12 May 2005 10:43:46 -0700 Subject: [DAS2] imported data into bug tracker Message-ID: I think the zmap client Ed Griffiths is talking about is going to be implemented in C or C++. Ed? gregg > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Allen Day > Sent: Thursday, May 12, 2005 10:40 AM > To: Andrew Dalke > Cc: DAS/2 > Subject: Re: [DAS2] imported data into bug tracker > > Is there a distiction made between these in CVS, i.e. are they in separate > repositories? Have you considered implementing some client components in > C? The reason I ask is that I'm interested in having a .so to link to so > that I can use a common DAS client API from R, Java, and Perl as well. > > -Allen > > On Thu, 12 May 2005, Andrew Dalke wrote: > > > Gregg: > > > The validation suite might be an exception to this distinction. I > > > doubt > > > that anyone else will reimplement this, and I think it's okay for it > to > > > be more tightly associated with the spec. > > > > Except that I've broken the validation code into two components. > > One is a das2 Python client and the other is the validator. And > > people may use the das2 component without using the validator. > > > > 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 edgrif at sanger.ac.uk Thu May 12 14:02:11 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Thu, 12 May 2005 19:02:11 +0100 (BST) Subject: [DAS2] imported data into bug tracker In-Reply-To: References: Message-ID: All, > I think the zmap client Ed Griffiths is talking about is going to be > implemented in C or C++. Ed? The zmap is implemented in C. Most of the code would not be appropriate to be implemented as a .so file but..... zmap (our client) is structured like this: ------ file reader | GUI ----- generalised -----|------ acedb server interface data source | interface | |------ DAS2 server interface | etc the DAS2 server interface could be to a C based parser written as a .so library...we have to write the code to do the parsing so it could potentially form the basis of a DAS2 C parser... I say "potentially" because I would need to think about how much work it would be as we are on a pretty tight schedule for the rest of the work... But a good idea... Ed > > Is there a distiction made between these in CVS, i.e. are they in > separate > > repositories? Have you considered implementing some client components > in > > C? The reason I ask is that I'm interested in having a .so to link to > so > > that I can use a common DAS client API from R, Java, and Perl as well. -- ** PLEASE NOTE NEW ADDRESS/PHONE NUMBER ** ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus | | Hinxton, Cambridge CB10 1HH | | | | email: edgrif at sanger.ac.uk Tel: +44-1223-496844 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From dalke at dalkescientific.com Thu May 12 14:08:39 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Thu, 12 May 2005 12:08:39 -0600 Subject: [DAS2] imported data into bug tracker In-Reply-To: References: <7abcba93337b0cf722a57c946ad89a0c@dalkescientific.com> Message-ID: <2c364bf8bc9867d7a47afb772d2665fa@dalkescientific.com> Allen: > Is there a distiction made between these in CVS, i.e. are they in > separate > repositories? Separate modules, same repository. > Have you considered implementing some client components in > C? The reason I ask is that I'm interested in having a .so to link to > so > that I can use a common DAS client API from R, Java, and Perl as well. No, not at all. That would be hard to do. I'm using some Python specific technologies, like the ElementTree parser to handle XML. I also have rather polymorphic code ("duck typing" at its best) that would be hard to port easily into C. I've found there's a much lower uptake of a given module if it requires a C extension. It's also not covered by the grant. Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Fri May 13 13:40:44 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 13 May 2005 11:40:44 -0600 Subject: [DAS2] imported data into bug tracker In-Reply-To: References: Message-ID: <2366abf6bb5fdbab595cb20839328a54@dalkescientific.com> Ed: > the DAS2 server interface could be to a C based parser written as a .so > library...we have to write the code to do the parsing so it could > potentially > form the basis of a DAS2 C parser... Hopefully you'll pull out one of the existing XML parsers instead of writing your own in C. Getting everything right is tricky, from what I understand. Especially when dealing with the various encoding issues (latin-1, utf-8, etc.) You'll end up building your own data types, I assume. Will that include things like a native date/time type or will clients need to parse the ISO string locally? I assume it's passed a string? If not, will it take a FILE *? Or will it be able to do the network connections too? If the latter, how will it work with proxies and other tedious details? If it's just a string then client libraries will still have to do some implementation work. My library will try to fix up known problems, eg, massage the input XML if it comes from a server that's known to have certain bugs. Supporting these in C would be, I think, a lot of work. Though if you used libxml2 and kept the data structure as its DOM and didn't worry about I/O ... Hmmm.... Andrew dalke at dalkescientific.com From Steve_Chervitz at affymetrix.com Fri May 13 14:24:51 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Fri, 13 May 2005 11:24:51 -0700 Subject: [DAS2] hackathon and das2 In-Reply-To: Message-ID: Ed: > > Is there any interest in doing DAS2 stuff at the proposed biohackathon in June > ? The hackathon is being cancelled due to not enough people being able to attend *both* the WWDC and the hackathon, a stipulation of Apple, who also was not able to provide any travel funds. The short notice and the proximity of BOSC just 10 days after it also made things difficult. Apple does have interest in doing something for 2006, but nothing definite yet. > I have someone in my team, Roy Storey, who could come out to work on our > client > (zmap) and making it work with das2. Is anyone else interested/going to this ? > > If people are interested it would be good to know soon as we will need to put > in > travel applications etc. etc. > > > Also, could someone add Roy (rds at sanger.ac.uk) to the das2 mailing list, > thanks. Done. Steve From suzi at fruitfly.org Mon May 16 20:26:00 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Mon, 16 May 2005 17:26:00 -0700 Subject: [DAS2] Fwd: [Fwd: Proposal for subcontract] Message-ID: Gregg (or Steve, or Lincoln) Who is the point person (grant administrator that is) at Affy that manages this? Or is the grant administered from CSH? We have to get moving on this here. I need to introduce our administrator to your administrator. -S Begin forwarded message: > From: Rob Quinlan > Date: May 16, 2005 4:26:37 PM PDT > To: Suzanna Lewis > Cc: Suzanna E Lewis , Nomi Harris > , Sima Misra > Subject: Re: [Fwd: Proposal for subcontract] > > Hello Suzanna, Nomi, & Sima, > > Please provide a name.? An administrative person at the other > institution as a point of contact. > This is somewhat urgent.... you never know what data they will ask > for & we need sufficient time to do it > > Thank you > Rob > ? > > > > Suzanna Lewis wrote: >> Hi Rob, >> >> Thanks for checking in. We are still planning are doing >> this submission. What is the LBL deadline? I've cc-ed >> a couple of other people who will be working with me >> on this, and (importantly) have said that they could help >> with getting you the material you need. I'll still be the >> single point of contact (so your life is easier), but if they >> are included on the exchanges they can be my Jiminy >> Cricket's with getting the material. >> >> -S >> >> On May 15, 2005, at 3:09 PM, Rob Quinlan wrote: >> >>> >>> >>> Have you had a chance to consider your grant submission? I was told >>> it is a subcontract that you are proposing. >>> This is a very busy time for proposals.... I just want to follow up >>> to ensure that you are included in a list we are keeping to handle >>> the excessive number of submissions. >>> >>> Thank you >>> Rob >>> >>> >>> -------- Original Message -------- >>> Subject: >>> Proposal for subcontract >>> Date: >>> Wed, 11 May 2005 15:30:27 -0700 >>> From: >>> Rob quinlan >>> Organization: >>> Lawrence Berkeley National Laboratory >>> To: >>> SELewis at lbl.gov >>> >>> >>> Hi Dr. Lewis: >>> >>> I have been assigned to assist you with your June 15th proposal >>> (subcontract). The internal deadline for an NIH subcontract would be >>> June 7th. >>> >>> In oder to prepare for this, please provide me with the name of the >>> other institution and a point of contact (an administrative person >>> please). Given the excessive workload of this department, it would >>> be >>> great to get ahead of this - so an early reply would be greatly >>> appreciated >>> >>> Thank you >>> Rob Quinlan >>> 495-2506 >>> >>> -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3080 bytes Desc: not available URL: From Gregg_Helt at affymetrix.com Tue May 17 00:56:17 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Mon, 16 May 2005 21:56:17 -0700 Subject: [DAS2] RE: [Fwd: Proposal for subcontract] Message-ID: The point person here at Affymetrix will be Katie Kong (katherine_kong at affymetrix.com), who is the grant administrator here for the current DAS/2 grant. For those of you on the das2 mailing list wondering, what we're talking about is submitting a proposal for continuation of the DAS/2 grant. The continuation would kick in (hopefully) in June 2006 when the current DAS/2 grant is scheduled to expire. gregg -----Original Message----- From: Suzanna Lewis [mailto:suzi at fruitfly.org] Sent: Monday, May 16, 2005 5:26 PM To: Helt,Gregg Cc: Nomi Harris; das2 at portal.open-bio.org; Sima Misra Subject: Fwd: [Fwd: Proposal for subcontract] Gregg (or Steve, or Lincoln) Who is the point person (grant administrator that is) at Affy that manages this? Or is the grant administered from CSH? We have to get moving on this here. I need to introduce our administrator to your administrator. -S Begin forwarded message: From: Rob Quinlan Date: May 16, 2005 4:26:37 PM PDT To: Suzanna Lewis Cc: Suzanna E Lewis , Nomi Harris , Sima Misra Subject: Re: [Fwd: Proposal for subcontract] Hello Suzanna, Nomi, & Sima, Please provide a name. An administrative person at the other institution as a point of contact. This is somewhat urgent.... you never know what data they will ask for & we need sufficient time to do it Thank you Rob Suzanna Lewis wrote: Hi Rob, Thanks for checking in. We are still planning are doing this submission. What is the LBL deadline? I've cc-ed a couple of other people who will be working with me on this, and (importantly) have said that they could help with getting you the material you need. I'll still be the single point of contact (so your life is easier), but if they are included on the exchanges they can be my Jiminy Cricket's with getting the material. -S On May 15, 2005, at 3:09 PM, Rob Quinlan wrote: Have you had a chance to consider your grant submission? I was told it is a subcontract that you are proposing. This is a very busy time for proposals.... I just want to follow up to ensure that you are included in a list we are keeping to handle the excessive number of submissions. Thank you Rob -------- Original Message -------- Subject: Proposal for subcontract Date: Wed, 11 May 2005 15:30:27 -0700 From: Rob quinlan Organization: Lawrence Berkeley National Laboratory To: SELewis at lbl.gov Hi Dr. Lewis: I have been assigned to assist you with your June 15th proposal (subcontract). The internal deadline for an NIH subcontract would be June 7th. In oder to prepare for this, please provide me with the name of the other institution and a point of contact (an administrative person please). Given the excessive workload of this department, it would be great to get ahead of this - so an early reply would be greatly appreciated Thank you Rob Quinlan 495-2506 From Gregg_Helt at affymetrix.com Tue May 17 01:02:25 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Mon, 16 May 2005 22:02:25 -0700 Subject: [DAS2] RE: Fwd: [Fwd: Proposal for subcontract] Message-ID: I've attached the DAS/2 grant proposal (submitted to NIH in February 2003). gregg > -----Original Message----- > From: Nomi Harris [mailto:nomi at fruitfly.org] > Sent: Monday, May 16, 2005 6:29 PM > To: Suzanna Lewis > Cc: Helt,Gregg; Nomi Harris; das2 at portal.open-bio.org; Sima Misra > Subject: Re: Fwd: [Fwd: Proposal for subcontract] > > Another thing we need in order to start writing the grant renewal is a > copy of the original grant application (preferably online rather than > just paper). > Nomi > > On 16 May 2005, Suzanna Lewis wrote: > > Gregg (or Steve, or Lincoln) > > > > Who is the point person (grant administrator that is) > > at Affy that manages this? Or is the grant administered > > from CSH? We have to get moving on this here. I need > > to introduce our administrator to your administrator. > > > > -S -------------- next part -------------- A non-text attachment was scrubbed... Name: Das2GrantFinalB.doc Type: application/msword Size: 355840 bytes Desc: Das2GrantFinalB.doc URL: From suzi at fruitfly.org Tue May 17 13:15:57 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Tue, 17 May 2005 10:15:57 -0700 Subject: [DAS2] Re: [Fwd: Proposal for subcontract] In-Reply-To: References: Message-ID: <0395dda68d0ccd979a082088c1952e2c@fruitfly.org> Thanks Gregg, On May 16, 2005, at 10:02 PM, Helt,Gregg wrote: > I've attached the DAS/2 grant proposal (submitted to NIH in February > 2003). > > gregg > >> -----Original Message----- >> From: Nomi Harris [mailto:nomi at fruitfly.org] >> Sent: Monday, May 16, 2005 6:29 PM >> To: Suzanna Lewis >> Cc: Helt,Gregg; Nomi Harris; das2 at portal.open-bio.org; Sima Misra >> Subject: Re: Fwd: [Fwd: Proposal for subcontract] >> >> Another thing we need in order to start writing the grant renewal is a >> copy of the original grant application (preferably online rather than >> just paper). >> Nomi >> >> On 16 May 2005, Suzanna Lewis wrote: >>> Gregg (or Steve, or Lincoln) >>> >>> Who is the point person (grant administrator that is) >>> at Affy that manages this? Or is the grant administered >>> from CSH? We have to get moving on this here. I need >>> to introduce our administrator to your administrator. >>> >>> -S > > From dalke at dalkescientific.com Tue May 17 14:14:10 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 17 May 2005 12:14:10 -0600 Subject: [DAS2] xml and compact formats Message-ID: <1cbb88669b42f0abefdfdc99d680787e@dalkescientific.com> Can someone remind me why we support both XML and "compact" formats? For what I'm doing it complicates things. Was it because of space/verbosity concerns? If so, should we encourage people to use compression on the connections? Andrew dalke at dalkescientific.com From Steve_Chervitz at affymetrix.com Tue May 17 15:10:31 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Tue, 17 May 2005 12:10:31 -0700 Subject: [DAS2] Non-genome DAS templates In-Reply-To: Message-ID: Cool. This adds functionality that goes beyond the scope of the original DAS/2 grant. So we'll have to make it clear that the current spec covers only genome template DAS, but that other templates are possible. This could be an appropriate area to discuss in the DAS/2 renewal. Steve > From: Allen Day > Date: Tue, 17 May 2005 18:39:56 +0000 > To: > Subject: [Gmod-das2-cmts] das2/lib/Bio/Das2/Source/Chado SthCache.pm,1.3,1.4 > > Update of /cvsroot/gmod/das2/lib/Bio/Das2/Source/Chado > In directory > sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23107/lib/Bio/Das2/Source/Chado > > Modified Files: > SthCache.pm > Log Message: > path changes now work. we can implement non-genome das templates now > From allenday at ucla.edu Tue May 17 18:31:00 2005 From: allenday at ucla.edu (Allen Day) Date: Tue, 17 May 2005 15:31:00 -0700 (PDT) Subject: [DAS2] Re: Non-genome DAS templates In-Reply-To: References: Message-ID: yes. as many of you know, i'm implementing a 'matrix' das domain space where you can retrieve the cross product of two other spaces. this is appropriate for, as a concrete example, retrieving a 2-dimensional matrix of measurements of genome features across a series of biological samples (e.g. a microarray). -allen On Tue, 17 May 2005, Chervitz, Steve wrote: > Cool. This adds functionality that goes beyond the scope of the original > DAS/2 grant. So we'll have to make it clear that the current spec covers > only genome template DAS, but that other templates are possible. > > This could be an appropriate area to discuss in the DAS/2 renewal. > > Steve > > > > From: Allen Day > > Date: Tue, 17 May 2005 18:39:56 +0000 > > To: > > Subject: [Gmod-das2-cmts] das2/lib/Bio/Das2/Source/Chado SthCache.pm,1.3,1.4 > > > > Update of /cvsroot/gmod/das2/lib/Bio/Das2/Source/Chado > > In directory > > sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23107/lib/Bio/Das2/Source/Chado > > > > Modified Files: > > SthCache.pm > > Log Message: > > path changes now work. we can implement non-genome das templates now > > > > From suzi at fruitfly.org Wed May 18 14:39:43 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Wed, 18 May 2005 11:39:43 -0700 Subject: [DAS2] DAS/2 grant conf call at 12 PST tomorrow In-Reply-To: References: Message-ID: Hi all, I had dinner with Lincoln last night to discuss the grant and we would like to move tomorrow's call (Thursday May 19) to noon. This is so that Lincoln can make the call. He has group meeting at the earlier time. The other alternative is to have 2 calls. Lincoln really wants to talk with us, Gregg. We also discussed some new aims for the renewal. This would make the existing grant quite a bit larger, but I think that is fine (based on conversations with Peter Good). These are some of the ideas we can talk over tomorrow. 1. Extend specification to include SNP data (contact Steve Sherry at dbSNP) 2. Extend specification to include protein structure data (contact Helen Berman at PDB) 3. Include an analysis server 4. Utilize the established Apollo and GMOD community to form a core of biologists that will actually commit to using DAS2 for the annotation of their organism and the merged apollo-igb (e.g. paramecium?, dictyostelium?) 5. Enable apollo-igb to act as both client and server? 6.... -S From Gregg_Helt at affymetrix.com Wed May 18 15:23:06 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Wed, 18 May 2005 12:23:06 -0700 Subject: [DAS2] RE: DAS/2 grant conf call at 12 PST tomorrow Message-ID: Changing the conference call to noon PST tomorrow sounds good to me. Callin number: USA domestic: 800-531-3250 International: 303-928-2693 Conference ID: 2879055 thanks, gregg > -----Original Message----- > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > Sent: Wednesday, May 18, 2005 11:40 AM > To: Helt,Gregg > Cc: > Subject: DAS/2 grant conf call at 12 PST tomorrow > > Hi all, > > I had dinner with Lincoln last night to discuss the grant > and we would like to move tomorrow's call (Thursday > May 19) to noon. This is so that Lincoln can make the > call. He has group meeting at the earlier time. The other > alternative is to have 2 calls. Lincoln really wants to > talk with us, Gregg. > > We also discussed some new aims for the renewal. > This would make the existing grant quite a bit larger, > but I think that is fine (based on conversations with > Peter Good). These are some of the ideas we can > talk over tomorrow. > > 1. Extend specification to include SNP data > (contact Steve Sherry at dbSNP) > 2. Extend specification to include protein structure data > (contact Helen Berman at PDB) > 3. Include an analysis server > 4. Utilize the established Apollo and GMOD community > to form a core of biologists that will actually commit to > using DAS2 for the annotation of their organism and > the merged apollo-igb > (e.g. paramecium?, dictyostelium?) > 5. Enable apollo-igb to act as both client and server? > 6.... > > -S From lstein at cshl.edu Wed May 18 15:57:04 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Wed, 18 May 2005 15:57:04 -0400 Subject: [DAS2] RE: DAS/2 grant conf call at 12 PST tomorrow In-Reply-To: References: Message-ID: <200505181557.04441.lstein@cshl.edu> Great! Lincoln On Wednesday 18 May 2005 03:23 pm, Helt,Gregg wrote: > Changing the conference call to noon PST tomorrow sounds good to me. > > Callin number: > USA domestic: 800-531-3250 > International: 303-928-2693 > Conference ID: 2879055 > > thanks, > gregg > > > -----Original Message----- > > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > Sent: Wednesday, May 18, 2005 11:40 AM > > To: Helt,Gregg > > Cc: > > Subject: DAS/2 grant conf call at 12 PST tomorrow > > > > Hi all, > > > > I had dinner with Lincoln last night to discuss the grant > > and we would like to move tomorrow's call (Thursday > > May 19) to noon. This is so that Lincoln can make the > > call. He has group meeting at the earlier time. The other > > alternative is to have 2 calls. Lincoln really wants to > > talk with us, Gregg. > > > > We also discussed some new aims for the renewal. > > This would make the existing grant quite a bit larger, > > but I think that is fine (based on conversations with > > Peter Good). These are some of the ideas we can > > talk over tomorrow. > > > > 1. Extend specification to include SNP data > > (contact Steve Sherry at dbSNP) > > 2. Extend specification to include protein structure data > > (contact Helen Berman at PDB) > > 3. Include an analysis server > > 4. Utilize the established Apollo and GMOD community > > to form a core of biologists that will actually commit to > > using DAS2 for the annotation of their organism and > > the merged apollo-igb > > (e.g. paramecium?, dictyostelium?) > > 5. Enable apollo-igb to act as both client and server? > > 6.... > > > > -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 edgrif at sanger.ac.uk Thu May 19 04:09:58 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Thu, 19 May 2005 09:09:58 +0100 (BST) Subject: [DAS2] DAS/2 grant conf call at 12 PST tomorrow In-Reply-To: References: Message-ID: Suzanna, > 4. Utilize the established Apollo and GMOD community > to form a core of biologists that will actually commit to > using DAS2 for the annotation of their organism and > the merged apollo-igb > (e.g. paramecium?, dictyostelium?) Although I'm not part of the grant application I think it would be good to widen this section to include those that don't use Apollo/gmod but could use das2, i.e. sanger, much of which uses acedb based systems of one sort or another. Ed -- ** PLEASE NOTE NEW ADDRESS/PHONE NUMBER ** ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus | | Hinxton, Cambridge CB10 1HH | | | | email: edgrif at sanger.ac.uk Tel: +44-1223-496844 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From Gregg_Helt at affymetrix.com Thu May 19 10:47:56 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 19 May 2005 07:47:56 -0700 Subject: [DAS2] xml and compact formats Message-ID: For the DAS/2 query for features, I think the ability to support alternative response formats is critical. Yes, this is mainly because of performance issues -- time to generate the XML on the server, time to deliver it over the network, time to parse it and memory footprint on the client side. Standard compression of the XML format is certainly possible, and unless we explicitly forbid it in the spec I see no reason why this can't be declared via the standard Accept-Encoding/Content-Encoding HTTP headers. But consider if network bandwidth is not the bottleneck (for example within an intranet or between sites connected to the Internet2 backbone). Compressing with gzip etc. will actually slow things down, requiring compression on the server and decompression on the client, and not speeding up actual client parsing at all. From experience I can tell you that the decompression cost on the client can be significant. Furthermore, more specific binary formats can be much smaller than compressed das2feature XML. For an extreme example, with an optimized format my client can parse in ~ 1 million SNP annotations per second. And yes, sometimes I need to do that. However, although I think the ability to _support_ alternative feature formats is critical, I don't think we should be declaring a set of alternative feature formats in the specification. We definitely need to have the ability for a server to generate and the client to accept annotation formats that the spec itself knows nothing about. All that is needed is a way for the server to indicate which formats it provides, and the client to choose which one it wants. In the current spec the server indicates which feature formats it supports for a particular versioned source as subelements under a "Feature types" element in the versioned source response. I would like to change this so that the formats supported are specific to the type of feature. This can be done by adding subelements to the elements in the types response. This would allow different alternative formats for different feature types, which I think is necessary -- a format optimized for SNPs is not going to be appropriate for serving up BLAT results, and vice versa. Now as far as the "compact" formats for other (non-feature) responses from the server, I don't think they're necessary. As far as performance issues, the size of these responses are unlikely to be anywhere near as large as the potential responses from a features request. So to summarize, I think the spec definitely needs to support a mechanism for alternative feature formats, but that it should be agnostic as to what those formats are. And I don't think we really need alternative formats for non-feature responses. 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: Tuesday, May 17, 2005 11:14 AM > To: DAS/2 > Subject: [DAS2] xml and compact formats > > Can someone remind me why we support both XML and "compact" > formats? For what I'm doing it complicates things. Was it > because of space/verbosity concerns? If so, should we > encourage people to use compression on the connections? > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From lstein at cshl.edu Thu May 19 12:44:09 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 19 May 2005 12:44:09 -0400 Subject: [DAS2] xml and compact formats In-Reply-To: References: Message-ID: <200505191244.10215.lstein@cshl.edu> I agree with Gregg on this. There are, for instance, several compact versions of XML that use a binary encoding for each tag and attribute. Lincoln On Thursday 19 May 2005 10:47 am, Helt,Gregg wrote: > For the DAS/2 query for features, I think the ability to support > alternative response formats is critical. Yes, this is mainly because > of performance issues -- time to generate the XML on the server, time to > deliver it over the network, time to parse it and memory footprint on > the client side. > > Standard compression of the XML format is certainly possible, and unless > we explicitly forbid it in the spec I see no reason why this can't be > declared via the standard Accept-Encoding/Content-Encoding HTTP headers. > But consider if network bandwidth is not the bottleneck (for example > within an intranet or between sites connected to the Internet2 > backbone). Compressing with gzip etc. will actually slow things down, > requiring compression on the server and decompression on the client, and > not speeding up actual client parsing at all. From experience I can > tell you that the decompression cost on the client can be significant. > Furthermore, more specific binary formats can be much smaller than > compressed das2feature XML. For an extreme example, with an optimized > format my client can parse in ~ 1 million SNP annotations per second. > And yes, sometimes I need to do that. > > However, although I think the ability to _support_ alternative feature > formats is critical, I don't think we should be declaring a set of > alternative feature formats in the specification. We definitely need to > have the ability for a server to generate and the client to accept > annotation formats that the spec itself knows nothing about. All that > is needed is a way for the server to indicate which formats it provides, > and the client to choose which one it wants. In the current spec the > server indicates which feature formats it supports for a particular > versioned source as subelements under a "Feature types" > element in the versioned source response. I would like to > change this so that the formats supported are specific to the type of > feature. This can be done by adding subelements to the > elements in the types response. This would allow different alternative > formats for different feature types, which I think is necessary -- a > format optimized for SNPs is not going to be appropriate for serving up > BLAT results, and vice versa. > > Now as far as the "compact" formats for other (non-feature) responses > from the server, I don't think they're necessary. As far as performance > issues, the size of these responses are unlikely to be anywhere near as > large as the potential responses from a features request. > > So to summarize, I think the spec definitely needs to support a > mechanism for alternative feature formats, but that it should be > agnostic as to what those formats are. And I don't think we really need > alternative formats for non-feature responses. > > 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: Tuesday, May 17, 2005 11:14 AM > > To: DAS/2 > > Subject: [DAS2] xml and compact formats > > > > Can someone remind me why we support both XML and "compact" > > formats? For what I'm doing it complicates things. Was it > > because of space/verbosity concerns? If so, should we > > encourage people to use compression on the connections? > > > > 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 -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From suzi at fruitfly.org Thu May 19 12:54:21 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Thu, 19 May 2005 09:54:21 -0700 Subject: [DAS2] DAS/2 grant conf call at 12 PST tomorrow In-Reply-To: References: Message-ID: I agree. Mostly want to tap into communities of biologists that would use a DAS in earnest. Any identifiable group we now know of is a good place to start. -S On May 19, 2005, at 1:09 AM, Ed Griffiths wrote: > Suzanna, > > >> 4. Utilize the established Apollo and GMOD community >> to form a core of biologists that will actually commit to >> using DAS2 for the annotation of their organism and >> the merged apollo-igb >> (e.g. paramecium?, dictyostelium?) > > Although I'm not part of the grant application I think it would be > good to widen > this section to include those that don't use Apollo/gmod but could use > das2, > i.e. sanger, much of which uses acedb based systems of one sort or > another. > > > Ed > > -- > ** PLEASE NOTE NEW ADDRESS/PHONE NUMBER ** > > > ----------------------------------------------------------------------- > - > | Ed Griffiths, Acedb development, Informatics Group, > | > | The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus > | > | Hinxton, Cambridge CB10 1HH > | > | > | > | email: edgrif at sanger.ac.uk Tel: +44-1223-496844 Fax: > +44-1223-494919 | > > ----------------------------------------------------------------------- > - From bugzilla-admin-daemon at portal.open-bio.org Thu May 19 12:52:35 2005 From: bugzilla-admin-daemon at portal.open-bio.org (bugzilla-admin-daemon at portal.open-bio.org) Date: Thu, 19 May 2005 12:52:35 -0400 Subject: [DAS2] Bugzilla Change Password Request Message-ID: <200505191652.j4JGqZe4032717@portal.open-bio.org> You (or someone impersonating you) has requested to change your Bugzilla password. To change your password, visit the following link: http://bugzilla.open-bio.org/token.cgi?a=cfmpw&t=DK4i4oah If you are not the person who made this request, or you wish to cancel this request, visit the following link: http://bugzilla.open-bio.org/token.cgi?a=cxlpw&t=DK4i4oah If you do nothing, the request will lapse after 3 days () or when you log in successfully. From dalke at dalkescientific.com Thu May 19 14:45:24 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Thu, 19 May 2005 12:45:24 -0600 Subject: [DAS2] Bugzilla and dasypus status In-Reply-To: <200505191652.j4JGqZe4032717@portal.open-bio.org> References: <200505191652.j4JGqZe4032717@portal.open-bio.org> Message-ID: <123f050e493a506e72e529ea9ea30336@dalkescientific.com> With Steve's help I've set up Bugzilla so that das2 at portal.open-bio.org is the primary owner of all problems. This means people should be able to update the web page and have copies of the changes sent to the mailing list. Except that it looks there's a minor change that needs to be made to Mailman to allow bugzilla-daemon at portal.open-bio.org to send email to the list. I just asked Steve to look at that. If anyone needs it, the Bugzilla password for das2 at portal.open-bio.org is "das2-password" In dasypus I changed the architecture to support different formats for a given request, because that was the spec. (Still needed for the features.) I also worked on code to be able to probe the input stream from the server and change things if there was a problem. Eg, last week's version of the server (haven't checked things this week) didn't emit proper XML. I wanted to be able to patch it and work. Based on my DAS/1 experience I know that that's not uncommon. In the next week I plan to finish off the support for probing and modifying the input stream, and get back to cleaning up the spec based on the various changes in the bug db. Here are the new bugs entered during the last week. 1797 nor P2 All das2 at portal.open-bio.org NEW don't need compact formats for non-feature requests 1798 nor P2 All das2 at portal.open-bio.org NEW add a subelement to for type-specific for... 1799 nor P2 All das2 at portal.open-bio.org NEW server should put server type & version in the HTTP headers 1800 nor P2 All dalke at dalkescientific.com NEW include comment about content-encoding Andrew dalke at dalkescientific.com From Steve_Chervitz at affymetrix.com Thu May 19 14:54:17 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Thu, 19 May 2005 11:54:17 -0700 Subject: [DAS2] Bugzilla and dasypus status In-Reply-To: <123f050e493a506e72e529ea9ea30336@dalkescientific.com> Message-ID: Andrew: > Except that it looks there's a minor change that needs to be > made to Mailman to allow bugzilla-daemon at portal.open-bio.org > to send email to the list. I just asked Steve to look at that. bugzilla-daemon at portal.open-bio.org has been successfully subscribed to DAS2. Steve From allenday at ucla.edu Fri May 20 05:26:31 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 20 May 2005 02:26:31 -0700 (PDT) Subject: [DAS2] RE: DAS/2 grant conf call at 12 PST tomorrow In-Reply-To: <200505181557.04441.lstein@cshl.edu> References: <200505181557.04441.lstein@cshl.edu> Message-ID: Is this a permanent change, or temporary? Is the conference id change permanent or temporary? -Allen On Wed, 18 May 2005, Lincoln Stein wrote: > Great! > > Lincoln > > On Wednesday 18 May 2005 03:23 pm, Helt,Gregg wrote: > > Changing the conference call to noon PST tomorrow sounds good to me. > > > > Callin number: > > USA domestic: 800-531-3250 > > International: 303-928-2693 > > Conference ID: 2879055 > > > > thanks, > > gregg > > > > > -----Original Message----- > > > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > > Sent: Wednesday, May 18, 2005 11:40 AM > > > To: Helt,Gregg > > > Cc: > > > Subject: DAS/2 grant conf call at 12 PST tomorrow > > > > > > Hi all, > > > > > > I had dinner with Lincoln last night to discuss the grant > > > and we would like to move tomorrow's call (Thursday > > > May 19) to noon. This is so that Lincoln can make the > > > call. He has group meeting at the earlier time. The other > > > alternative is to have 2 calls. Lincoln really wants to > > > talk with us, Gregg. > > > > > > We also discussed some new aims for the renewal. > > > This would make the existing grant quite a bit larger, > > > but I think that is fine (based on conversations with > > > Peter Good). These are some of the ideas we can > > > talk over tomorrow. > > > > > > 1. Extend specification to include SNP data > > > (contact Steve Sherry at dbSNP) > > > 2. Extend specification to include protein structure data > > > (contact Helen Berman at PDB) > > > 3. Include an analysis server > > > 4. Utilize the established Apollo and GMOD community > > > to form a core of biologists that will actually commit to > > > using DAS2 for the annotation of their organism and > > > the merged apollo-igb > > > (e.g. paramecium?, dictyostelium?) > > > 5. Enable apollo-igb to act as both client and server? > > > 6.... > > > > > > -S > > > > _______________________________________________ > > DAS2 mailing list > > DAS2 at portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/das2 > > From Steve_Chervitz at affymetrix.com Fri May 20 21:11:20 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Fri, 20 May 2005 18:11:20 -0700 Subject: [DAS2] Bugzilla and dasypus status In-Reply-To: <123f050e493a506e72e529ea9ea30336@dalkescientific.com> Message-ID: The das2 mailman account for bugzilla was disabled since, apparently, it didn't like receiving the messages it's been getting every time someone posts to the das/2 list: List: DAS2 Member: bugzilla-admin-daemon at portal.open-bio.org Action: Subscription disabled. Reason: Excessive or fatal bounces. I've re-enabled the account and turned off message delivery to this and the bugzilla-daemon account. So it should be back in action, but I haven't tested it. We only need this to be one-way connection: bugzilla sends messages to the das/2 mailman list, not vice versa. Steve > From: Andrew Dalke > Date: Thu, 19 May 2005 12:45:24 -0600 > To: DAS/2 > Subject: [DAS2] Bugzilla and dasypus status > > With Steve's help I've set up Bugzilla so that das2 at portal.open-bio.org > is the primary owner of all problems. This means people should be > able to update the web page and have copies of the changes sent > to the mailing list. > > Except that it looks there's a minor change that needs to be > made to Mailman to allow bugzilla-daemon at portal.open-bio.org > to send email to the list. I just asked Steve to look at that. > > If anyone needs it, the Bugzilla password for das2 at portal.open-bio.org > is "das2-password" > > In dasypus I changed the architecture to support different > formats for a given request, because that was the spec. (Still > needed for the features.) I also worked on code to be able to > probe the input stream from the server and change things if > there was a problem. Eg, last week's version of the server > (haven't checked things this week) didn't emit proper XML. > I wanted to be able to patch it and work. Based on my DAS/1 > experience I know that that's not uncommon. > > In the next week I plan to finish off the support for probing > and modifying the input stream, and get back to cleaning up > the spec based on the various changes in the bug db. > > Here are the new bugs entered during the last week. > > 1797 nor P2 All das2 at portal.open-bio.org NEW don't need compact > formats for non-feature requests > > 1798 nor P2 All das2 at portal.open-bio.org NEW add a subelement > to for type-specific for... > > 1799 nor P2 All das2 at portal.open-bio.org NEW server should put server > type & version in the HTTP headers > > 1800 nor P2 All dalke at dalkescientific.com NEW include comment about > content-encoding > > > 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 Thu May 26 14:29:32 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Thu, 26 May 2005 12:29:32 -0600 Subject: [DAS2] dasypus status Message-ID: <8c9ccda9007b66475af2d280e2b39405@dalkescientific.com> The major client architecture is complete. Finally. It's all in CVS. I started work on updating the spec based on the changes in the bug tracking system, previous discussion, and my experience in implementing the client. I noticed that there was no real introduction or overview section so I started writing that. I would like to merge all of the docs into one. The current split is hard to read because: - one is for the general protocol - one is for GET - one is for writeback - nothing is for general overview/concepts. Keeping it as 3 or 4 pages makes it hard to read, and hard to search. I've started working on the validator proper but it's on hold. Here are some of the warnings generated so far against the prototype server WARNING: Adding X-DAS-Server header 'gmod/0.0' The prototype doesn't mention the DAS server used. I stick one in based on the host name. ERROR: Unknown content-type 'text/x-das-source+xml' for service 'sources' That should be "text/x-das-sources+xml" WARNING: Fixing DAS namespace {http://www.biodas.org/ns/das/2.00}; should be {http://www.biodas.org/ns/das/genome/2.00} WARNING: Fixing base of http://das.biopackages.net:0/das; should be http://das.biopackages.net/das/genome/ ERROR: Unknown content-type 'text/x-das-source-details+xml' for service 'detailed_source' That should be "text/x-das-version+xml", I think. WARNING: VERSION tag not closed There's a bug in the generated XML. Dasypus fixes it. Andrew dalke at dalkescientific.com From bugzilla-daemon at portal.open-bio.org Thu May 26 14:57:30 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 26 May 2005 14:57:30 -0400 Subject: [DAS2] [Bug 1803] New: indicate that two reference coordinate systems are the same Message-ID: <200505261857.j4QIvUYJ014139@portal.open-bio.org> 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. From bugzilla-daemon at portal.open-bio.org Fri May 27 02:20:07 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 27 May 2005 02:20:07 -0400 Subject: [DAS2] [Bug 1807] New: Where do seqids come from? Message-ID: <200505270620.j4R6K71h021749@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1807 Summary: Where do seqids come from? 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 Did a stork drop them off in the cabbage patch? I'm trying to understand regions and their relationship to sequence. The spec says > seqid is the sequence ID, and can correspond to an assembled chromosome, a > contig, a clone, or any other accessionable chunk of sequence Is the seqid exactly equivalent to a region id? I think so given the documentation in das2_protocol.html. The das2_protocol.html document also says > http://server/das/genome/sourceid/version/region/regionid/subregion > A genomic region region identified by the ID of a landmark, modified by > a subregion relative to the landmark. As a whole, the URL is a globally > unique identifier for a region of the genome. > > The syntax of addressing regions and subregions is described in detail later. The das2_get.html document says > Adding a subregion restricts the document further to regions that overlap the indicated subregion. > > REQUEST: > > GET http://server/das/genome/sourceid/version/region/ctg2 > or > GET http://server/das/genome/sourceid/version/region/ctg2/34/128 What are the '24' and '128'? Are they coordinate ranges? Are they independently accessionable chunks of the genome, so that .../sequence/34?format=fasta is valid? Or do I get the sequence via .../sequence/ctg2/34/?format=fasta ------- 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 Fri May 27 02:05:19 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 27 May 2005 02:05:19 -0400 Subject: [DAS2] [Bug 1806] New: When should DAS/2 URLs end with a '/'? Message-ID: <200505270605.j4R65Jwo021604@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1806 Summary: When should DAS/2 URLs end with a '/'? 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 Consider the following http://www.biodas.org/das/genome/human/0/type http://www.biodas.org/das/genome/human/0/region http://www.biodas.org/das/genome/human/0/feature vs. http://www.biodas.org/das/genome/human/0/type/ http://www.biodas.org/das/genome/human/0/region/ http://www.biodas.org/das/genome/human/0/feature/ Which is to be preferred? Should one be required to redirect to the other and if so, which way? I waver between the two. One the one hand, the first grouping makes it easier to understand it when parameters are passed to the URL. .../region?format=agp .../feature?type=exon By comparison, the following looks strange, though legitimate .../region/?format=agp .../feature/?type=exon I did some research on this. One site says http://www.markbaker.ca/2002/01/UriOpacityInvestigation/ ============ The one standout thing about "/" when compared with the other separators, is that has a special meaning in the context of relative and base URI processing. Relative URI are only relative because they are hierarchical. That is, "/wow/gee" is a relative URI, but when grounded to a base URI of; http://example.org/foo/ yields an absolute URI of; http://example.org/foo/wow/gee This suggests that URI publishers should be concerned about whether their URI end in "/" or not. If the URI might ever be used as a container, it should end with "/". This also suggests that the relationship between a URI with a terminating slash, and the same URI without the terminating slash, is also nothing more than that same non-specific hierarchical relationship. ============= In that case we should be using '/' for most of the URLs. A problem comes in with subregions to a region. When does a subregion name end with a '/'? Eg, if the following exists (assuming there are no children under 128) .../region/ctg2/34/128 then what about .../region/ctg2 ? On a system with writeback support will someone ever be able to create a sub-part? I assume not. Similarly, the following would not be appropriate .../sequence/Contig2 because there's always the chance of selecting a range from it .../sequence/Contig2/1000:2000 This is an ambiguity in the PUT spec as well. Consider one lock request section which specifies filter_href="feature?overlaps=Chr3/1000:500000" and another which specifies POST http://dev.wormbase.org/das/genome/volvox/1/feature/?lock=xyzzy My current belief is: - all of the namespaces ("sequence/", "region/", "feature/", ...) must end with a "/". This means we will have URLs like .../region/ChrX/?format=das2xml .../feature/?type=exon - the assembly will not change for a given version so we specify that anything with a subregion must be referenced with a '/' and the server must redirect names that are missing the '/'. Terminal regions must not end with a '/'. - Terminals (the actual feature, lock, etc.) must not end with a '/'. The odd one out is the .../sequence/ namespace. Is .../sequence/Contig1 ever allowed, given that clients may use .../sequence/Contig1/200:350 ? Note, btw, that sequence/ ranges are one of the few parts of the DAS spec which is not REST-ful, because it violates the idea that URLs are opaque to the client, excepting for '?' query parameters. ------- 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 Fri May 27 02:25:22 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 27 May 2005 02:25:22 -0400 Subject: [DAS2] [Bug 1808] New: , region ids and sequence ids Message-ID: <200505270625.j4R6PMMK021838@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1808 Summary: , region ids and sequence ids 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 In bug 1807 I asked how region ids are related to sequence ids. I think they are supposed to be the same, so to get the sequence for a given region you append the region id to the sequence namespace. How does the client know which namespace to use? I think it's supposed to be hard-coded into the client that "/sequence/" contains the genomic DNA. Otherwise there is insufficient information in the versioned source request to figure out which URL to use. Consider this example from the spec There's not enough information for the client to figure out that the "volvox/1/sequence" URL contains genomic sequences while the "volvox/1/protein" contains protein sequences. I would rather have a 'type' field where the type data is from a well-defined vocabulary. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From edgrif at sanger.ac.uk Tue May 3 13:47:43 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Tue, 3 May 2005 14:47:43 +0100 (BST) Subject: [DAS2] more updates to das2 docs In-Reply-To: References: Message-ID: All, I've made a couple of changes to the docs in the das2 sub directory... 1) I've made the protocol doc into a template style doc, this means that all the das2 docs in that directory follow the same pattern of preparation: das2_XXX_template.html --- munging by Andrews stuff --> das2_XXX.html in other words: only edit the das2_XXX_template.html docs. It also means you can now write separate xml docs for the examples in the text and have those verified and incorporated via Andrews stuff. 2) I've put some new DAS/2 response codes into das2_protocol_template.html, these directly follow the existing section on response codes as a table of codes. Please do read/mark/inwardly digest. Ed -- ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif at sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From dalke at dalkescientific.com Wed May 4 06:58:05 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Wed, 4 May 2005 00:58:05 -0600 Subject: [DAS2] hrefs and xml:base Message-ID: <4adee633f9ac4385a8757e7533fdfacc@dalkescientific.com> Do the 'href' and 'doc_href' fields obey the xml:base directive or only the "id" fields? Andrew dalke at dalkescientific.com From edgrif at sanger.ac.uk Wed May 4 08:48:01 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Wed, 4 May 2005 09:48:01 +0100 (BST) Subject: [DAS2] Re: [DAS] Hackathon 2005 In-Reply-To: References: Message-ID: Suzanna, Hi, we met at Hinxton last autumn I think. I've been doing more stuff on DAS2 with Lincoln and it may be that there are people who would like to do stuff on DAS2. I've been working away on a replacement for xace/fmap which is called zmap and would like it to use the DAS2 protocol. To this end I have someone called Roy Storey (who is on vacation at the moment) in my group who may well be interested in being part of a DAS2 hacking group. I'm copying him and also the das2 mailing list on this. As soon as Roy gets back I will talk to him about it. Ed On Wed, 20 Apr 2005, Suzanna Lewis wrote: > (sorry for multiple postings, but please do forward to > anyone else who you think might be interested) > > ------------------------------------------------------------------------ > ----------- > > Dear everyone, > > It has been a long time and we Bioinformatics devotees are overdue for > another total-immersion coding-fest (the last hackathon was held in > Singapore February 2003, more than two years ago). Apple has offered > to host us this year, and as an added bonus include free admission to > the World-Wide Developers Conference in San Francisco the prior week. > They are also looking for some people to present interesting new > developments at the WWDC, so if you have something noteworthy please > let us know. Apple is not attaching any strings, so our work need not > address Apple-specific software or hardware areas. Apple will provide > space and hardware (and access to their engineers if we'd like). > > Week 1 (June 6-10) would be spent at the WWDC. Week 2 (June 12-16) > would be in Cupertino, at Apple's headquarters. We're free to focus > on what interests us, our tentative plans include: > > 1. Bio-ontologies software > 2. High-performance computing (e.g. large scale computations, > optimization) > 3. Image analysis > 4. Documentation > 5. Anything else that may interest you > > Our plan is to organize this much as the Aspen Center for Physics > computational biology workshops were organized (for those old enough to > remember): A couple of presentations to start the day; collaboration > and coding afterwards; time for a bit of fun (does anyone else > cycle?), and discussions in the late afternoons and evenings. > > Would everyone who is interested in attending please send us a short > description of what you would like to do, and perhaps other people who > you would like to work with. There is somewhat limited space, so we > will try to prioritize groups that have a clear focus and a need to > interact. We now this is very short notice, but we hope that there > will be enough interest to make it possible. > > We are looking into additional funding support, to pay for travel > expenses, but this is still to be decided. > > Looking forward to hearing from everyone. > George, Cyrus, Steve, and Suzanna (the Bay Area locals) > > _______________________________________________ > DAS mailing list > DAS at biodas.org > http://biodas.org/mailman/listinfo/das > > > -- ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif at sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From dalke at dalkescientific.com Wed May 4 20:07:11 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Wed, 4 May 2005 14:07:11 -0600 Subject: [DAS2] das2 validator name Message-ID: Hi all, I've been working on the DAS2 validator. I'm trying to come up with a better name than "DAS2Check". The two names I've come up with so far are "Dascyllus" (a name for a type of damselfish) and "Dasypod" (the name for armadillos). The advantages are: - they have "Das" in the name :) - it's easy to get a pretty pictures for either - the phylogenetic name gives a loose tie to genomics - my test set can pull from existing sequences - I can't find any other software with either name - for "dascyllus", a friend of mine does research in damselfish phylogenies The disadvantages: - "dascyllus" sounds similar to "bacillus" - I had to ask that same friend how to pronounce "dasypod" ("da'-see-pod" and not "day-zy-pod") - a non-descriptive name requires one extra level of indirection. "DAS2Check" gives a clue as to what it does. I also came across "dasturi" which seems great given both the "DAS" and the "URI". But it means a tip or a bribe or skimming off the top. Perhaps "DasUri"? Hmm.... Since I'm having trouble, perhaps someone here has a better idea or a comment on the above ideas? Otherwise, I'm leaning towards Dasypod. Andrew dalke at dalkescientific.com From Gregg_Helt at affymetrix.com Wed May 4 20:15:23 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Wed, 4 May 2005 13:15:23 -0700 Subject: [DAS2] hrefs and xml:base Message-ID: If we want to fully adopt the xml:base standard (which I think we do), then my interpretation is that xml:base is lexically scoped and within its scope allows any attribute that requires a URI to be potentially specified as a relative URI (relative to the xml:base) instead of an absolute URI. So I would say "href", "doc_href", "id", and a number of other attributes should obey the xml:base directive(s). Note that this doesn't preclude using an absolute URI for these values, it just also allows using a relative URI. Here's a nice concise summary of xml:base : http://www.brics.dk/~amoeller/XML/common/xbase.html 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: Tuesday, May 03, 2005 11:58 PM > To: das2 at portal.open-bio.org > Subject: [DAS2] hrefs and xml:base > > Do the 'href' and 'doc_href' fields obey the xml:base > directive or only the "id" fields? > > > 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 Wed May 4 20:44:43 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Wed, 4 May 2005 13:44:43 -0700 Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? Message-ID: So we haven't had a big DAS/2 meeting since last September, and I'm feeling the need for one. I would like to propose we meet during the upcoming BOSC or ISMB conferences in Detroit (BOSC June 23-24, ISMB June 25-29). How many of us are already planning to attend one or both of these conferences? Thanks, Gregg From allenday at ucla.edu Wed May 4 21:09:05 2005 From: allenday at ucla.edu (Allen Day) Date: Wed, 4 May 2005 14:09:05 -0700 (PDT) Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? In-Reply-To: References: Message-ID: I will only be attending BOSC and the AltSplice SIG. If you'd like to meet just before or just after, that would work for me. -Allen On Wed, 4 May 2005, Helt,Gregg wrote: > So we haven't had a big DAS/2 meeting since last September, and I'm > feeling the need for one. I would like to propose we meet during the > upcoming BOSC or ISMB conferences in Detroit (BOSC June 23-24, ISMB June > 25-29). How many of us are already planning to attend one or both of > these conferences? > > Thanks, > Gregg > > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 > From dalke at dalkescientific.com Wed May 4 21:46:41 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Wed, 4 May 2005 15:46:41 -0600 Subject: [DAS2] hrefs and xml:base In-Reply-To: References: Message-ID: <8d6083fdc293785cf3646ac5ce8defc8@dalkescientific.com> Gregg: > If we want to fully adopt the xml:base standard (which I think we do), > then my interpretation is that xml:base is lexically scoped and within > its scope allows any attribute that requires a URI to be potentially > specified as a relative URI (relative to the xml:base) instead of an > absolute URI. That's what I figured, and what I did in my code. I'll edit the docs to flag which fields are expanded by xml:base. Now for part 2 of the question, in the tag will the values ever take relative URLs? Eg, suppose some server has an SVG description of how to draw the type In a related topic, the TYPES example we have says ... Is the "bg" in the XML namespace "bg" supposed to be inserted into the key name as a string? If so, how? Using universal names ( http://www.jclark.com/xml/xmlns.htm ) like "{http://www.bioperl.org/biographics/properties}height" Or is the xmlns:bg definition there in error? This is a problem for me because the parsers I use treat XML namespaces as things that only apply to tags and attributes and throw away the namespace scope. There aren't that many people using DAS nor will there be. We could just say that certain prefixes are reserved and that people may pick a unused namespace prefix as desired. Andrew dalke at dalkescientific.com From Steve_Chervitz at affymetrix.com Wed May 4 21:51:00 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Wed, 04 May 2005 16:51:00 -0500 Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? In-Reply-To: Message-ID: I'll be at both BOSC and ISMB. Meeting somewhere in between these, or during the evenings of the BOSC days would work best for me. Steve > From: Allen Day > Date: Wed, 4 May 2005 14:09:05 -0700 (PDT) > To: "Helt,Gregg" > Cc: > Subject: Re: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? > > I will only be attending BOSC and the AltSplice SIG. If you'd like to > meet just before or just after, that would work for me. > > -Allen > > On Wed, 4 May 2005, Helt,Gregg wrote: > >> So we haven't had a big DAS/2 meeting since last September, and I'm >> feeling the need for one. I would like to propose we meet during the >> upcoming BOSC or ISMB conferences in Detroit (BOSC June 23-24, ISMB June >> 25-29). How many of us are already planning to attend one or both of >> these conferences? >> >> Thanks, >> Gregg >> >> >> _______________________________________________ >> 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 Wed May 4 22:10:26 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Wed, 4 May 2005 23:10:26 +0100 Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? In-Reply-To: References: Message-ID: I'll be there (back to the native grounds for me) I arrive on the 23rd and stay for duration. -S On May 4, 2005, at 9:44 PM, Helt,Gregg wrote: > So we haven't had a big DAS/2 meeting since last September, and I'm > feeling the need for one. I would like to propose we meet during the > upcoming BOSC or ISMB conferences in Detroit (BOSC June 23-24, ISMB > June > 25-29). How many of us are already planning to attend one or both of > these conferences? > > Thanks, > Gregg > > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From dalke at dalkescientific.com Wed May 4 22:35:49 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Wed, 4 May 2005 16:35:49 -0600 Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? In-Reply-To: References: Message-ID: <568e85a31dd8baa6f2018fbc4e8fba8d@dalkescientific.com> Gregg: > I would like to propose we meet during the upcoming BOSC or ISMB > conferences in Detroit (BOSC June 23-24, ISMB June 25-29). How > many of us are already planning to attend one or both of > these conferences? I will be there. Andrew dalke at dalkescientific.com From ed_erwin at affymetrix.com Wed May 4 23:55:11 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Wed, 04 May 2005 16:55:11 -0700 Subject: [DAS2] hrefs and xml:base In-Reply-To: <8d6083fdc293785cf3646ac5ce8defc8@dalkescientific.com> References: <8d6083fdc293785cf3646ac5ce8defc8@dalkescientific.com> Message-ID: <427960DF.6090400@affymetrix.com> Andrew Dalke wrote: > > In a related topic, the TYPES example we have says > > xmlns="http://www.biodas.org/ns/das/genome/2.00" > xmlns:xlink="http://www.w3.org/1999/xlink" > xmlns:bg="http://www.bioperl.org/biographics/properties" > xmlns:das="http://www.biodas.org/ns/das/genome/2.00" > xml:base="http://www.wormbase.org/das/genome/volvox/1/type/"> > ... > > > > > > > > > Is the "bg" in the XML namespace "bg" supposed to be inserted > into the key name as a string? If so, how? Using universal > names ( http://www.jclark.com/xml/xmlns.htm ) like > "{http://www.bioperl.org/biographics/properties}height" > > Or is the xmlns:bg definition there in error? > I also wondered about this. I assumed that the "bg:" is a mistake, because later there is an example of this feature type request: http://www.wormbase.org/das/genome/volvox/1/type/tRNAscan/citation Here, ".../citation" is used, rather than ".../bg:citation", but it is my understanding that the key is supposed to literally map to the name used in constructing that type request URL. I have two other question/comments on that document ( http://biodas.org/documents/das2/das2_get.html ): > (zero or more) > indicates which representations are available for objects > within the given namespace. Does this mean *all* objects in the given namespace will be available in *all* of the given format ? or that *some* will be available in each of the listed formats ? In the example response to this query, the "sequence-ontology" header is commented-out for no good reason: http://www.wormbase.org/das/genome/volvox/1/type/tRNAscan?format=compact From lstein at cshl.edu Wed May 4 23:59:04 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Wed, 4 May 2005 19:59:04 -0400 Subject: [DAS2] hrefs and xml:base In-Reply-To: <8d6083fdc293785cf3646ac5ce8defc8@dalkescientific.com> References: <8d6083fdc293785cf3646ac5ce8defc8@dalkescientific.com> Message-ID: <200505041959.04164.lstein@cshl.edu> Hi, I think that the current spec uses xml:base in the way that the standard intends, but please feel free to insert clarifications & corrections. As far as putting the bg: prefix into the key name, it was intended to indicate that the key "glyph" belongs to the list of properties located at http://www.bioperl.org/biographics/properties. Now, I didn't find any references to tell me how to namespace an attribute value, so I just fudged things. Are there better ways to do this? Lincoln On Wednesday 04 May 2005 17:46, Andrew Dalke wrote: > Gregg: > > If we want to fully adopt the xml:base standard (which I think we do), > > then my interpretation is that xml:base is lexically scoped and within > > its scope allows any attribute that requires a URI to be potentially > > specified as a relative URI (relative to the xml:base) instead of an > > absolute URI. > > That's what I figured, and what I did in my code. > > I'll edit the docs to flag which fields are expanded by xml:base. > > Now for part 2 of the question, in the tag will > the values ever take relative URLs? Eg, suppose some > server has an SVG description of how to draw the type > > > > In a related topic, the TYPES example we have says > > xmlns="http://www.biodas.org/ns/das/genome/2.00" > xmlns:xlink="http://www.w3.org/1999/xlink" > xmlns:bg="http://www.bioperl.org/biographics/properties" > xmlns:das="http://www.biodas.org/ns/das/genome/2.00" > xml:base="http://www.wormbase.org/das/genome/volvox/1/type/"> > .. > > > > > > > > > Is the "bg" in the XML namespace "bg" supposed to be inserted > into the key name as a string? If so, how? Using universal > names ( http://www.jclark.com/xml/xmlns.htm ) like > "{http://www.bioperl.org/biographics/properties}height" > > Or is the xmlns:bg definition there in error? > > This is a problem for me because the parsers I use treat > XML namespaces as things that only apply to tags and attributes > and throw away the namespace scope. > > There aren't that many people using DAS nor will there > be. We could just say that certain prefixes are reserved > and that people may pick a unused namespace prefix as desired. > > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From lstein at cshl.edu Wed May 4 23:59:33 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Wed, 4 May 2005 19:59:33 -0400 Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? In-Reply-To: References: Message-ID: <200505041959.34065.lstein@cshl.edu> I'll be there for BOSC, but I'm not sure about ISMB, so during BOSC would be the safer bet. Lincoln On Wednesday 04 May 2005 17:51, Chervitz, Steve wrote: > I'll be at both BOSC and ISMB. Meeting somewhere in between these, or > during the evenings of the BOSC days would work best for me. > > Steve > > > From: Allen Day > > Date: Wed, 4 May 2005 14:09:05 -0700 (PDT) > > To: "Helt,Gregg" > > Cc: > > Subject: Re: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? > > > > I will only be attending BOSC and the AltSplice SIG. If you'd like to > > meet just before or just after, that would work for me. > > > > -Allen > > > > On Wed, 4 May 2005, Helt,Gregg wrote: > >> So we haven't had a big DAS/2 meeting since last September, and I'm > >> feeling the need for one. I would like to propose we meet during the > >> upcoming BOSC or ISMB conferences in Detroit (BOSC June 23-24, ISMB June > >> 25-29). How many of us are already planning to attend one or both of > >> these conferences? > >> > >> Thanks, > >> Gregg > >> > >> > >> _______________________________________________ > >> 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 Thu May 5 00:30:53 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Wed, 4 May 2005 20:30:53 -0400 Subject: [DAS2] hrefs and xml:base In-Reply-To: <427960DF.6090400@affymetrix.com> References: <8d6083fdc293785cf3646ac5ce8defc8@dalkescientific.com> <427960DF.6090400@affymetrix.com> Message-ID: <200505042030.53717.lstein@cshl.edu> On Wednesday 04 May 2005 19:55, Ed Erwin wrote: > Andrew Dalke wrote: > > In a related topic, the TYPES example we have says > > > > > xmlns="http://www.biodas.org/ns/das/genome/2.00" > > xmlns:xlink="http://www.w3.org/1999/xlink" > > xmlns:bg="http://www.bioperl.org/biographics/properties" > > xmlns:das="http://www.biodas.org/ns/das/genome/2.00" > > xml:base="http://www.wormbase.org/das/genome/volvox/1/type/"> > > ... > > > > > > > > > > > > > > > > > > Is the "bg" in the XML namespace "bg" supposed to be inserted > > into the key name as a string? If so, how? Using universal > > names ( http://www.jclark.com/xml/xmlns.htm ) like > > "{http://www.bioperl.org/biographics/properties}height" > > > > Or is the xmlns:bg definition there in error? > > I also wondered about this. > > I assumed that the "bg:" is a mistake, because later there is an example > of this feature type request: > > http://www.wormbase.org/das/genome/volvox/1/type/tRNAscan/citation > > Here, ".../citation" is used, rather than ".../bg:citation", but it is > my understanding that the key is supposed to literally map to the > name used in constructing that type request URL. > > > I have two other question/comments on that document ( > > http://biodas.org/documents/das2/das2_get.html ): > > (zero or more) > > indicates which representations are available for objects > > within the given namespace. > > Does this mean *all* objects in the given namespace will be available in > *all* of the given format ? or that *some* will be available in each of > the listed formats ? All objects in the given namespace will be available in all of the given formats. Lincoln From dalke at dalkescientific.com Thu May 5 16:42:35 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Thu, 5 May 2005 10:42:35 -0600 Subject: [DAS2] Dasypus status Message-ID: (See, I'm trying out one of the possible names) I've implemented the core architecture over the last few days. It took some head-banging, and sadly not the fun kind. The result is somewhat sweet. The difficulty was because I wanted to test the various sorts of things that could go wrong. This include: - HTTP server doesn't respond, infinite loop, etc. - the wrong values in the HTTP headers (eg, wrong version) - invalid XML returned [1] - wrong elements in the XML [2] - wrong fields in the XML [3] [1] We should add a new DAS header which is the server version. Eg, some of the DAS/1 servers returned invalid XML, like when the "&" attribute needs to be escaped. I want to allow a cleanup, triggered on the server type, that fixes these sorts of errors. [2] While the schema can catch these, some are errors while others (like extending the XML) should be warnings. [3] For example, the prototype server uses the wrong namespace and wrong xml:base. I've told Allen about it but in the meanwhile I've put a host-based cleanup filter in place. In addition several layers of the architecture are easily exchangeable with others. For example: - the "URL opener" is replaceable. This lets me put in test code to check that the URL of a request is as expected, lets me wrote a standalone proxy system to use local files for http requests, and potentially lets someone implement, say, an interface that reads directly from a MySQL connection instead of going through the web. (Hmmm, interesting ... I had just thought of that possibility.) - the "builder" layer is replaceable. This is the one that in most apps takes the input socket connection and makes a usable data structure from it. I have one builder for Python data structures. I'll soon have one for the schema checker and another that allows both builders to work. - the "build a Python data structure" knows that a few data structures are special and could be converted into something other than a string or integer. One example is the ISO date, which by default gets turned into a Python datetime. Another is a link from one part of DAS to another. By default it's a string but I experimented with a version that fetches the given link on request, which makes the data structure act like a direct mirror of the DAS object network. In doing this I noticed a couple of problems with the DAS XML we have. I've pointed out a couple. I'm in the process of cleaning up a few others. I am able to read all of the XML in the DAS CVS repository and Allen's SOURCES url. The server has been down the last few days and I haven't been able to get any further. The next steps for me are: - we were going to change the section of the spec, right? What were the changes? - check Dasypus into CVS - implements builders for the RNG validation and to let both the RNG and Python data structure builders work. - finish the error/warning handling code - clean up the example XML files - start developing test sets - work with Allen's prototype server - implement the handler for the compact formats (Again, what's the reason for the compact formats?) All that is to check that a request/response works. The next stage is to check for system integrity. I'm not close enough to that yet to describe the steps involved. Andrew dalke at dalkescientific.com From ed_erwin at affymetrix.com Thu May 5 17:26:02 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Thu, 05 May 2005 10:26:02 -0700 Subject: [DAS2] Questions on the DAS2 spec Message-ID: <427A572A.9040904@affymetrix.com> I recently re-read the document http://biodas.org/documents/das2/das2_protocol.html#overview It is looking pretty good. But there were areas that I didn't understand, and others that I want to comment on. I'll post my questions/comments one-per-email to make discussion easier. - First issue: I'd like to clear-up the requirements for the base URL. All URL examples begin something like this: http://server/das/..... Is it permissable for "server" to contain "/" characters? Is it permissable to use "https://" instead of "http://" Is it really required that the string "/das/" be part of the url? It would be useful, mainly for testing purposes, to be able to run multiple DAS2 servers on a single IP address, like this: http://netaffxdas.affymetrix.com/public/das/ https://netaffxdas.affymetrix.com/private/das/ http://netaffxdas.affymetrix.com/testing/das2/ http://netaffxdas.affymetrix.com:9091/testing/das/ Thus "server" needs to be able to include un-escaped "/" characters, and maybe even ":" for designating ports. Maybe that was already intended, but there are no such examples given in the spec. I'd rather replace all the URL examples with http(s)://urlbase/... where urlbase can contain "/" and does not necessarily have to include the string "/das/". In particular, some places that already have a DAS1 server running on "/das" may want to use "/das2" for any new server. Cheers, Ed From ed_erwin at affymetrix.com Thu May 5 17:37:59 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Thu, 05 May 2005 10:37:59 -0700 Subject: [DAS2] DAS status codes Message-ID: <427A59F7.20003@affymetrix.com> My next set of questions/comments on http://biodas.org/documents/das2/das2_protocol.html#overview are about the status codes. >> X-DAS-Status: XXX status code The spec should make a point of mentioning that the X-DAS-Status header code is NOT the same as HTTP status codes. Even when the X-DAS-Status code is 501 (indicating an error), the HTTP status code should be 200 (indicating that the DAS server actually heard and responded to the request). (This is because the HTTP status codes already have specific meanings and the software packages that the clients use to access the web may notice those codes and take unwanted actions as a result.) - Codes 201 and 205 seem redundant, or else I don't understand the distinction. - Can we consider 200,400,500 to be a generic OK/CLIENT ERROR/SERVER ERROR response when the server doesn't know how to return a more specific 2xx,4xx,5xx code? This would mean changing the definition of "400" which is currently listed as > 400 == The request could not be understood by the server due to malformed syntax. In keeping with the idea that codes ending in "00" are generic, I suggest 400 == "Bad request (not otherwise specified)." and we would need a new code for "malformed syntax". From ed_erwin at affymetrix.com Thu May 5 17:39:11 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Thu, 05 May 2005 10:39:11 -0700 Subject: [DAS2] Data Source Request Message-ID: <427A5A3F.5010805@affymetrix.com> More comments on http://biodas.org/documents/das2/das2_protocol.html#overview In the data source request, http://server/das/genome/sourceid it says > sourceid and version can be any combination of characters Hmmm, are all characters really OK? Even "/" ? Shouldn't it state "sourceid and version can contain any combination of URLEncoded characters. From ed_erwin at affymetrix.com Thu May 5 17:43:45 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Thu, 05 May 2005 10:43:45 -0700 Subject: [DAS2] Meeting Message-ID: <427A5B51.6020901@affymetrix.com> I may be a little late for the meeting this morning, but I will call in when I can. Gregg should initiate the conference call from his phone. 1-800-531-3250 id 2879055 From lstein at cshl.edu Thu May 5 19:39:12 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 5 May 2005 15:39:12 -0400 Subject: [DAS2] DAS2 phone call schedules Message-ID: <200505051539.12196.lstein@cshl.edu> Could someone send me the schedule for the calls, and the number to call in from? Thanks, Lincoln From lstein at cshl.edu Thu May 5 19:44:19 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 5 May 2005 15:44:19 -0400 Subject: [DAS2] Dasypus status In-Reply-To: References: Message-ID: <200505051544.19121.lstein@cshl.edu> > The next steps for me are: > - we were going to change the section of the > spec, right? What were the changes? I don't know! What *were* the changes? Lincoln > > - check Dasypus into CVS > > - implements builders for the RNG validation and to > let both the RNG and Python data structure builders work. > > - finish the error/warning handling code > > - clean up the example XML files > > - start developing test sets > > - work with Allen's prototype server > > - implement the handler for the compact formats > (Again, what's the reason for the compact formats?) > > All that is to check that a request/response works. > The next stage is to check for system integrity. > I'm not close enough to that yet to describe the > steps involved. > > 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 Thu May 5 20:22:35 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 5 May 2005 13:22:35 -0700 Subject: [DAS2] DAS2 phone call schedules Message-ID: Apologies, I thought I had posted that info before! DAS/2 grant weekly teleconference, Thursdays at 11:30 AM Pacific time. Conference call-in number: USA: 800-531-3250 International: 303-928-2693 Conference id: 2879055 In general in this meeting we're covering a lot of ground: implementation details and progress, spec issues, organizational stuff, etc. I'd really like to start breaking this down so that we have at least one teleconference a month that focuses on just the actual DAS/2 specification and that the principals from the different sites can all attend. Then we can focus on other topics (implementation etc.) during the other weekly meetings, which not everyone would need to attend. Best compromise time for the monthly meeting so far is 10 AM Fridays. Which is still difficult for Hinxton, so I'm open to other suggestions. 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: Thursday, May 05, 2005 12:39 PM > To: das2 at portal.open-bio.org > Subject: [DAS2] DAS2 phone call schedules > > Could someone send me the schedule for the calls, and the number to call > in > from? > > Thanks, > > Lincoln > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From lstein at cshl.edu Thu May 5 20:22:51 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 5 May 2005 16:22:51 -0400 Subject: [DAS2] das2 validator name In-Reply-To: References: Message-ID: <200505051622.51510.lstein@cshl.edu> How about "Das boot"? Lincoln On Wednesday 04 May 2005 16:07, Andrew Dalke wrote: > Hi all, > > I've been working on the DAS2 validator. I'm trying to > come up with a better name than "DAS2Check". The two > names I've come up with so far are "Dascyllus" (a name for > a type of damselfish) and "Dasypod" (the name for armadillos). > > The advantages are: > - they have "Das" in the name :) > - it's easy to get a pretty pictures for either > - the phylogenetic name gives a loose tie to genomics > - my test set can pull from existing sequences > - I can't find any other software with either name > > - for "dascyllus", a friend of mine does research > in damselfish phylogenies > > The disadvantages: > - "dascyllus" sounds similar to "bacillus" > - I had to ask that same friend how to pronounce "dasypod" > ("da'-see-pod" and not "day-zy-pod") > - a non-descriptive name requires one extra level of > indirection. "DAS2Check" gives a clue as to what it does. > > > I also came across "dasturi" which seems great given both > the "DAS" and the "URI". But it means a tip or a bribe or > skimming off the top. Perhaps "DasUri"? Hmm.... > > Since I'm having trouble, perhaps someone here has a better > idea or a comment on the above ideas? Otherwise, I'm > leaning towards Dasypod. > > 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 Thu May 5 20:30:00 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 5 May 2005 13:30:00 -0700 Subject: [DAS2] das2 validator name Message-ID: Good one, I'm changing my vote from Dasypod to Das Boot! 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: Thursday, May 05, 2005 1:23 PM > To: das2 at portal.open-bio.org > Subject: Re: [DAS2] das2 validator name > > How about "Das boot"? > > Lincoln > > On Wednesday 04 May 2005 16:07, Andrew Dalke wrote: > > Hi all, > > > > I've been working on the DAS2 validator. I'm trying to > > come up with a better name than "DAS2Check". The two > > names I've come up with so far are "Dascyllus" (a name for > > a type of damselfish) and "Dasypod" (the name for armadillos). > > > > The advantages are: > > - they have "Das" in the name :) > > - it's easy to get a pretty pictures for either > > - the phylogenetic name gives a loose tie to genomics > > - my test set can pull from existing sequences > > - I can't find any other software with either name > > > > - for "dascyllus", a friend of mine does research > > in damselfish phylogenies > > > > The disadvantages: > > - "dascyllus" sounds similar to "bacillus" > > - I had to ask that same friend how to pronounce "dasypod" > > ("da'-see-pod" and not "day-zy-pod") > > - a non-descriptive name requires one extra level of > > indirection. "DAS2Check" gives a clue as to what it does. > > > > > > I also came across "dasturi" which seems great given both > > the "DAS" and the "URI". But it means a tip or a bribe or > > skimming off the top. Perhaps "DasUri"? Hmm.... > > > > Since I'm having trouble, perhaps someone here has a better > > idea or a comment on the above ideas? Otherwise, I'm > > leaning towards Dasypod. > > > > 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 Steve_Chervitz at affymetrix.com Thu May 5 23:29:33 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Thu, 05 May 2005 16:29:33 -0700 Subject: [DAS2] das2 validator name In-Reply-To: Message-ID: I like Das Boot too (motto: ?Giving DAS a Boot?), but the armadillo symbolism is fitting since armadillos are very tough and robust, and that?s good symbolism for a validation suite. Here?s another more tenuous connection between DAS and armadillos: * Some folks connected with DAS come from Drosophila labs (Gregg, Suzi) * Drosophila embryos have genes that are expressed in a striped pattern, akin to the 9-banded armadillo (and there is a Drosophila gene called armadillo: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Grap hics&list_uids=31151 ) Steve > From: "Helt,Gregg" > Date: Thu, 5 May 2005 13:30:00 -0700 > To: Lincoln Stein , > Subject: RE: [DAS2] das2 validator name > > Good one, I'm changing my vote from Dasypod to Das Boot! > > 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: Thursday, May 05, 2005 1:23 PM >> To: das2 at portal.open-bio.org >> Subject: Re: [DAS2] das2 validator name >> >> How about "Das boot"? >> >> Lincoln >> >> On Wednesday 04 May 2005 16:07, Andrew Dalke wrote: >>> Hi all, >>> >>> I've been working on the DAS2 validator. I'm trying to >>> come up with a better name than "DAS2Check". The two >>> names I've come up with so far are "Dascyllus" (a name for >>> a type of damselfish) and "Dasypod" (the name for armadillos). >>> >>> The advantages are: >>> - they have "Das" in the name :) >>> - it's easy to get a pretty pictures for either >>> - the phylogenetic name gives a loose tie to genomics >>> - my test set can pull from existing sequences >>> - I can't find any other software with either name >>> >>> - for "dascyllus", a friend of mine does research >>> in damselfish phylogenies >>> >>> The disadvantages: >>> - "dascyllus" sounds similar to "bacillus" >>> - I had to ask that same friend how to pronounce "dasypod" >>> ("da'-see-pod" and not "day-zy-pod") >>> - a non-descriptive name requires one extra level of >>> indirection. "DAS2Check" gives a clue as to what it does. >>> >>> >>> I also came across "dasturi" which seems great given both >>> the "DAS" and the "URI". But it means a tip or a bribe or >>> skimming off the top. Perhaps "DasUri"? Hmm.... >>> >>> Since I'm having trouble, perhaps someone here has a better >>> idea or a comment on the above ideas? Otherwise, I'm >>> leaning towards Dasypod. >>> >>> 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 > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From ed_erwin at affymetrix.com Thu May 5 23:35:21 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Thu, 05 May 2005 16:35:21 -0700 Subject: [DAS2] das2 validator name In-Reply-To: References: Message-ID: <427AADB9.7050807@affymetrix.com> The first name I thought of myself was "Das Boot". I even started writing an e-mail to Andrew suggesting that name, but then I decided I was being too silly so I deleted it. Americans already mispronounce the "Boot" part of "Das Boot". Now we'll be encouraging the mispronounciation of "Das" as well. I like that ! Chervitz, Steve wrote: > I like Das Boot too (motto: ?Giving DAS a Boot?), From edgrif at sanger.ac.uk Fri May 6 06:00:23 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Fri, 6 May 2005 07:00:23 +0100 (BST) Subject: [DAS2] das2 validator name In-Reply-To: References: Message-ID: Andrew, how about Dastry, as in "Dastry rides again"....sorry, couldn't resist... Ed On Wed, 4 May 2005, Andrew Dalke wrote: > Hi all, > > I've been working on the DAS2 validator. I'm trying to > come up with a better name than "DAS2Check". The two > names I've come up with so far are "Dascyllus" (a name for > a type of damselfish) and "Dasypod" (the name for armadillos). > > The advantages are: > - they have "Das" in the name :) > - it's easy to get a pretty pictures for either > - the phylogenetic name gives a loose tie to genomics > - my test set can pull from existing sequences > - I can't find any other software with either name > > - for "dascyllus", a friend of mine does research > in damselfish phylogenies > > The disadvantages: > - "dascyllus" sounds similar to "bacillus" > - I had to ask that same friend how to pronounce "dasypod" > ("da'-see-pod" and not "day-zy-pod") > - a non-descriptive name requires one extra level of > indirection. "DAS2Check" gives a clue as to what it does. > > > I also came across "dasturi" which seems great given both > the "DAS" and the "URI". But it means a tip or a bribe or > skimming off the top. Perhaps "DasUri"? Hmm.... > > Since I'm having trouble, perhaps someone here has a better > idea or a comment on the above ideas? Otherwise, I'm > leaning towards Dasypod. > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 > > > -- ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif at sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From ed_erwin at affymetrix.com Fri May 6 17:16:03 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Fri, 06 May 2005 10:16:03 -0700 Subject: [DAS2] hrefs and xml:base In-Reply-To: References: Message-ID: <427BA653.3060807@affymetrix.com> The document you cite as defining xml:base leaves me with an unanswered question. It says that this is inspired by the html tag, but doesn't say whether it works in the same complex way that html works. Namely, with this base tag: This href: href="../cages/birds.gif" resolves to: http://www.aviary.com/cages/birds.gif In other words, it doesn't simply do a String concatenation of the base and the href, but rather has to throw away the "intro.html" part and interpret the meaning of ".." This example comes from http://www.w3.org/TR/REC-html40/struct/links.html#h-12.4 Is there some more complete specification of xml:base that states whether these complicated things are allowed? Helt,Gregg wrote: > If we want to fully adopt the xml:base standard (which I think we do), > then my interpretation is that xml:base is lexically scoped and within > its scope allows any attribute that requires a URI to be potentially > specified as a relative URI (relative to the xml:base) instead of an > absolute URI. > > So I would say "href", "doc_href", "id", and a number of other > attributes should obey the xml:base directive(s). Note that this > doesn't preclude using an absolute URI for these values, it just also > allows using a relative URI. > > Here's a nice concise summary of xml:base : > http://www.brics.dk/~amoeller/XML/common/xbase.html > From dalke at dalkescientific.com Fri May 6 17:39:59 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 6 May 2005 11:39:59 -0600 Subject: [DAS2] hrefs and xml:base In-Reply-To: <427BA653.3060807@affymetrix.com> References: <427BA653.3060807@affymetrix.com> Message-ID: <25d8222dbd7d513a5bd0a2ec5ac92999@dalkescientific.com> Ed: > Is there some more complete specification of xml:base that states > whether these complicated things are allowed? They are allowed. The xml:base can be contained in another xml:base and they interact as you described. The spec is at http://www.w3.org/TR/xmlbase/ Andrew dalke at dalkescientific.com From Steve_Chervitz at affymetrix.com Fri May 6 18:25:56 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Fri, 06 May 2005 11:25:56 -0700 Subject: [DAS2] hrefs and xml:base In-Reply-To: <25d8222dbd7d513a5bd0a2ec5ac92999@dalkescientific.com> Message-ID: As far as I can tell, there is no restriction that an xml:base URI must end with a /, but that seems to be the convention. In this case, constructing relative URLs by concatenating ../ onto the xml:base URI should work. Here?s an xml:base tutorial that has a bunch of examples, in all cases xml:base specifies a directory: http://www.zvon.org/xxl/XMLBaseTutorial/Output/index.html I did find an example of an xml:base that points to a file, but it?s on a MSDN site, making it therefore highly suspect: http://msdn.microsoft.com/library/default.asp?url=/library/en-us/dnxmlnet/ht ml/xinclude.asp BTW, the W3C recommendation http://www.w3.org/TR/xmlbase/ doesn't mention the use of ../ within an XML base spec. But since it's just a URI, it is allowed. See the URI spec: http://www.gbiv.com/protocols/uri/rfc/rfc3986.html#path Steve > From: Andrew Dalke > Date: Fri, 6 May 2005 11:39:59 -0600 > To: > Subject: Re: [DAS2] hrefs and xml:base > > Ed: >> Is there some more complete specification of xml:base that states >> whether these complicated things are allowed? > > They are allowed. The xml:base can be contained in another xml:base > and they interact as you described. > > The spec is at http://www.w3.org/TR/xmlbase/ > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From ed_erwin at affymetrix.com Fri May 6 18:30:00 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Fri, 06 May 2005 11:30:00 -0700 Subject: [DAS2] hrefs and xml:base In-Reply-To: <25d8222dbd7d513a5bd0a2ec5ac92999@dalkescientific.com> References: <427BA653.3060807@affymetrix.com> <25d8222dbd7d513a5bd0a2ec5ac92999@dalkescientific.com> Message-ID: <427BB7A8.7080908@affymetrix.com> Thanks. That also clears-up another question I had asked earlier (although I can't find the e-mail where I asked it.) Anyway, the question had come-up whether the contents of the 'id' attribute should be URLEncoded inside the xml document. Based on this xmlbase spec, the answer is NO. The contents of the id attributes should be XMLEncoded when necessary, but the URLEncoding will happen during the process of converting the attribute value to a URL. "processors must encode and escape these characters to obtain a valid URI reference from the attribute value" If the XML attribute value is already URLEncoded, this process would result in double-encoding. Andrew Dalke wrote: > Ed: > >> Is there some more complete specification of xml:base that states >> whether these complicated things are allowed? > > > They are allowed. The xml:base can be contained in another xml:base > and they interact as you described. > > The spec is at http://www.w3.org/TR/xmlbase/ > > 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 Sat May 7 05:12:36 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 6 May 2005 23:12:36 -0600 Subject: [DAS2] Dasypus status In-Reply-To: <200505051544.19121.lstein@cshl.edu> References: <200505051544.19121.lstein@cshl.edu> Message-ID: <0e0b66c022685cc27fd8579a8858817d@dalkescientific.com> Me: >> - we were going to change the section of the >> spec, right? What were the changes? Lincoln: > I don't know! What *were* the changes? Here's the current spec (zero or more) A property of this feature. Properties are typed using the ptype attribute. The value of the property may indicated by a URL given by the href attribute, or may be given inline as the CDATA content of the section. ptype ? a URL describing the property type href (optional) ? a URL that provides more information about the property of this feature, can be used for database XREFs mime_type (optional) ? MIME type of the CDATA contents content_encoding (optional) ? Encoding of the CDATA contents CDATA text ? Content The proposal was to get rid of the CDATA text. That makes things less complex, at the cost of a potential extra network lookup. We can get rid of the mime_type and content_encoding fields too. We don't need to have the extra lookup. A couple days ago I was reminded of the "data" URL scheme http://www.ietf.org/rfc/rfc2397.txt That RFC gives a couple of examples: data:,A%20brief%20note is the text/plain string "A brief note" Larry is an inline image of some bearded dude, in b&w. More info about the data URI scheme (dated) http://www.mozilla.org/quality/networking/docs/aboutdata.html with on-line examples at http://www.mozilla.org/quality/networking/testing/datatests.html Cool! Safari understands it! Actually, it seems that everyone except IE understand it these days. Anyway, using a data URL scheme lets us get rid of the CDATA, content_encoding and mime_type fields of the and still let us embed small chunks of data in-line. Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Tue May 10 08:10:38 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 10 May 2005 02:10:38 -0600 Subject: [DAS2] das2 validator name In-Reply-To: <200505051622.51510.lstein@cshl.edu> References: <200505051622.51510.lstein@cshl.edu> Message-ID: After considering the options I went for my first name - Dasypus. I applied for a new sf.net project. It was accepted: dasypus.sf.net I did an initial check-in of the Python code I've been working on. There will be two parts: - "das2"; a client library - "dasypus"; the validator I've been working on the client library, trying to figure out which parts go where. Eg, I discovered today I needed to support dumping the result information so I can track down and perhaps fix XML-level errors. In other news, I've been going through the back emails and moving spec proposals over to the new bug tracking database. Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Tue May 10 08:13:32 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 10 May 2005 02:13:32 -0600 Subject: [DAS2] das2 validator name In-Reply-To: References: Message-ID: Steve: > I like Das Boot too (motto: ?Giving DAS a Boot?), Along those lines I also considered "dastard". :) Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Tue May 10 08:46:20 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 10 May 2005 02:46:20 -0600 Subject: [DAS2] hrefs and xml:base In-Reply-To: References: Message-ID: <43fc505775bc621f56f249aa179ae65f@dalkescientific.com> Steve: > As far as I can tell, there is no restriction that an xml:base URI > must end with a /, but that seems to be the convention. > In this case, constructing relative URLs by concatenating ../ onto > the xml:base URI should work. If the URI doesn't end with a '/' then the last term will almost certainly be removed as part of the join. That is xml:base = "http://www.biodas.org/some/path/foo" id = "bar" should generate xml:base = "http://www.biodas.org/some/path/bar" Except for an empty id that last term ("foo") is needless. > I did find an example of an xml:base that points to a > file, but it?s on a > MSDN site, making it therefore highly suspect: > http://msdn.microsoft.com/library/default.asp?url=/library/en-us/ > dnxmlnet/html/xinclude.asp There's no problem having xml:base point to a file. > BTW, the W3C recommendation http://www.w3.org/TR/xmlbase/ > doesn't mention the use of ../ within an XML base spec. What it does is refer people to RFC 2396 for a description of how a base and relative URI interact. See section 5.2 of that spec for details. That RFC is document format independent. The xml:base spec describes how xml:base works in an XML document. The base URI of an element is: the base URI specified by an xml:base attribute on the element, if one exists, otherwise the base URI of the element's parent element within the document or external entity, if one exists, otherwise the base URI of the document entity or external entity containing the element. That's a recursive definition, so multiple xml:bases are allowed. Once the base and relative URI's are known, they are joined as defined in RFC 2396. Though I see now it's out of date. > But since it's just a URI, it is allowed. See the URI spec: > http://www.gbiv.com/protocols/uri/rfc/rfc3986.html#path RFC 3986 obsoletes the RFC 2396 mentioned in the xml:base spec. :) Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Tue May 10 10:32:14 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 10 May 2005 04:32:14 -0600 Subject: [DAS2] imported data into bug tracker Message-ID: I've imported all of the back emails for spec changes into the bug tracker at http://bugzilla.open-bio.org/ Here's the list ID Sev Pri Plt Owner State Result Summary 1783 nor P2 All lstein at cshl.org NEW requirements for the base URL 1784 nor P2 All lstein at cshl.org NEW status codes 1785 nor P2 All dalke at dalkescientific.com NEW clarify how to escape terms in the URL 1786 nor P2 All lstein at cshl.org NEW use data: URLs to simplify the tag 1787 nor P2 All dalke at dalkescientific.com NEW remove CAPABILITIES 1788 nor P2 All lstein at cshl.org NEW use "uri" instead of "id" 1789 nor P2 All lstein at cshl.org NEW use NameValueType 1790 nor P2 All lstein at cshl.org NEW ambiguity in "att=name:value" queries 1791 nor P2 All lstein at cshl.org NEW restrict a /type response to a subset of types 1792 nor P2 All lstein at cshl.org NEW allow 'type's which aren't derived from sofa 1793 nor P2 All dalke at dalkescientific.com NEW XML examples need a version string 1794 nor P2 All lstein at cshl.org NEW s in a 1795 nor P2 All lstein at cshl.org NEW bg: namespace in Andrew dalke at dalkescientific.com From Steve_Chervitz at affymetrix.com Tue May 10 19:14:01 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Tue, 10 May 2005 12:14:01 -0700 Subject: [DAS2] imported data into bug tracker In-Reply-To: Message-ID: Thanks for importing these Andrew. Jason Stajich graciously set up the DAS area in the open-bio bugzilla database for us. I was starting to add components to it. So far, there are only two, one for general spec issues and one for issues with the GET request portion of the spec. I was planning to add components for writeback portion of the spec, but haven't done that yet. I thought it might be convenient to use this bugzilla as a one-stop-shop for tracking all DAS/2 related bugs, including client, server, and validation suite. Forcing people to use different bug trackers for client, server, validation suite, and spec issues I think would be too unwieldy. Having one place to go would be easier for submitters and developers. How do folks feel about using this bugzilla db in this way? Steve > From: Andrew Dalke > Date: Tue, 10 May 2005 04:32:14 -0600 > To: > Subject: [DAS2] imported data into bug tracker > > I've imported all of the back emails for spec changes into > the bug tracker at http://bugzilla.open-bio.org/ > > Here's the list > > ID Sev Pri Plt Owner State Result Summary > 1783 nor P2 All lstein at cshl.org NEW requirements for the base URL > > 1784 nor P2 All lstein at cshl.org NEW status codes > > 1785 nor P2 All dalke at dalkescientific.com NEW clarify how to escape > terms in the URL > > 1786 nor P2 All lstein at cshl.org NEW use data: URLs to simplify the > tag > > 1787 nor P2 All dalke at dalkescientific.com NEW remove CAPABILITIES > > 1788 nor P2 All lstein at cshl.org NEW use "uri" instead of "id" > > 1789 nor P2 All lstein at cshl.org NEW use NameValueType > > 1790 nor P2 All lstein at cshl.org NEW ambiguity in "att=name:value" > queries > > 1791 nor P2 All lstein at cshl.org NEW restrict a /type response to a > subset of types > > 1792 nor P2 All lstein at cshl.org NEW allow 'type's which aren't derived > from sofa > > 1793 nor P2 All dalke at dalkescientific.com NEW XML examples need a > version string > > 1794 nor P2 All lstein at cshl.org NEW s in a > > 1795 nor P2 All lstein at cshl.org NEW bg: namespace in > > > 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 Tue May 10 19:55:58 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 10 May 2005 13:55:58 -0600 Subject: [DAS2] imported data into bug tracker In-Reply-To: References: Message-ID: <89cf814c18c217608fec492c2097e046@dalkescientific.com> Steve: > How do folks feel about using this bugzilla db [as the central > bug report system]? Fine with me. I don't think it needs to be broken down into GET and PUT components. For a small project like this I think that's too fine grained. Andrew dalke at dalkescientific.com From allenday at ucla.edu Tue May 10 20:22:10 2005 From: allenday at ucla.edu (Allen Day) Date: Tue, 10 May 2005 13:22:10 -0700 (PDT) Subject: [DAS2] imported data into bug tracker In-Reply-To: <89cf814c18c217608fec492c2097e046@dalkescientific.com> References: <89cf814c18c217608fec492c2097e046@dalkescientific.com> Message-ID: Andrew and I are putting server bugs into the sourceforge tracker, but I'd be happy to move them over to open-bio if it's easier for people. Although I personally like SF. -Allen On Tue, 10 May 2005, Andrew Dalke wrote: > Steve: > > How do folks feel about using this bugzilla db [as the central > > bug report system]? > > Fine with me. > > I don't think it needs to be broken down into GET and PUT > components. For a small project like this I think that's > too fine grained. > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 > From ed_erwin at affymetrix.com Tue May 10 20:25:46 2005 From: ed_erwin at affymetrix.com (Ed Erwin) Date: Tue, 10 May 2005 13:25:46 -0700 Subject: [DAS2] imported data into bug tracker In-Reply-To: References: Message-ID: <428118CA.1070300@affymetrix.com> Chervitz, Steve wrote: > I thought it might be convenient to use this bugzilla as a one-stop-shop for > tracking all DAS/2 related bugs, including client, server, and validation > suite. Please do NOT put IGB bugs in the DAS/2 bugzilla, even though it is intended to become a DAS/2 client. I already have to keep track of 3 bug-reporting repositories for IGB and I don't need a fourth one! But thanks, Andrew, for copying our e-mails over to that bugzilla. From Steve_Chervitz at affymetrix.com Tue May 10 22:10:19 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Tue, 10 May 2005 15:10:19 -0700 Subject: [DAS2] imported data into bug tracker In-Reply-To: <428118CA.1070300@affymetrix.com> Message-ID: Ed Erwin wrote: > Chervitz, Steve wrote: >> I thought it might be convenient to use this bugzilla as a one-stop-shop for >> tracking all DAS/2 related bugs, including client, server, and validation >> suite. > > Please do NOT put IGB bugs in the DAS/2 bugzilla, even though it is > intended to become a DAS/2 client. I already have to keep track of 3 > bug-reporting repositories for IGB and I don't need a fourth one! I also believe it is best to not migrate existing bugs from the established client and server bug trackers into the open-bio bugzilla db. However, there's a decent chance that people will submit new bugs on the open-bio bugzilla pertaining to anything related to DAS. Once people start getting their hands wet with DAS/2, they may naturally gravitate to bugzilla.open-bio.org, since it is close to biodas.org (in internet space). A good solution might be to have a Bugs link on biodas.org pointing to a page that describes where to go to submit/view bugs for various parts of DAS/2 that are being developed by the grant: * Bugs for the spec -> bugzilla.open-bio.org * Bugs for the IGB client -> genoviz.sf.net (or where?) * Bugs for the gmod server -> gmod.sf.net * Bugs for the validation suite -> ?? I can look into setting up this page. Steve From dalke at dalkescientific.com Wed May 11 06:23:29 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Wed, 11 May 2005 00:23:29 -0600 Subject: [DAS2] imported data into bug tracker In-Reply-To: References: Message-ID: <5263783bfe378dbb186ebeabf70daef9@dalkescientific.com> Steve: > A good solution might be to have a Bugs link on biodas.org pointing to > a > page that describes where to go to submit/view bugs for various parts > of > DAS/2 that are being developed by the grant: > > * Bugs for the spec -> bugzilla.open-bio.org > * Bugs for the IGB client -> genoviz.sf.net (or where?) > * Bugs for the gmod server -> gmod.sf.net > * Bugs for the validation suite -> ?? > > I can look into setting up this page. I personally have no preference. I can use the SF project bug tracker for Dasypus, or DAS/2 one. I can even use all 4 different trackers. I think people will tend to use the bug tracker mentioned on the main page for a given project, which can point wherever. If there is a mixup with a bug reported in the wrong system then it's easy enough to say "closed; moved to the XYZ tracker." But I honestly think there won't be that many mixups. Andrew dalke at dalkescientific.com From edgrif at sanger.ac.uk Wed May 11 14:07:33 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Wed, 11 May 2005 15:07:33 +0100 (BST) Subject: [DAS2] hackathon and das2 In-Reply-To: References: Message-ID: All, Is there any interest in doing DAS2 stuff at the proposed biohackathon in June ? I have someone in my team, Roy Storey, who could come out to work on our client (zmap) and making it work with das2. Is anyone else interested/going to this ? If people are interested it would be good to know soon as we will need to put in travel applications etc. etc. Also, could someone add Roy (rds at sanger.ac.uk) to the das2 mailing list, thanks. cheers Ed -- ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif at sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From allenday at ucla.edu Wed May 11 19:40:55 2005 From: allenday at ucla.edu (Allen Day) Date: Wed, 11 May 2005 12:40:55 -0700 (PDT) Subject: [DAS2] hackathon and das2 In-Reply-To: References: Message-ID: I'm interested to discuss DAS/2 at the biohackathon. On Wed, 11 May 2005, Ed Griffiths wrote: > All, > > Is there any interest in doing DAS2 stuff at the proposed biohackathon in June ? > > I have someone in my team, Roy Storey, who could come out to work on our client > (zmap) and making it work with das2. Is anyone else interested/going to this ? > > If people are interested it would be good to know soon as we will need to put in > travel applications etc. etc. > > > Also, could someone add Roy (rds at sanger.ac.uk) to the das2 mailing list, thanks. > > cheers Ed > From Gregg_Helt at affymetrix.com Thu May 12 14:44:09 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 12 May 2005 07:44:09 -0700 Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? Message-ID: Based on everyone's responses, it looks like there are more of us attending BOSC than ISMB. So I'd like to propose a tentative schedule: June 22, evening -- informal meeting, whoever gets there early. Dinner? June 23, afternoon/evening -- DAS/2 grantee meeting, open only to grant collaborators (basically everyone on this list) June 24, afternoon/evening -- DAS/2 BOF, open to anyone who wants to attend Thoughts? gregg P.S. I just received notice that the DAS/2 abstract I submitted for BOSC was accepted for presentation. Hopefully that will generate interest in the BOF. > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Helt,Gregg > Sent: Wednesday, May 04, 2005 1:45 PM > To: das2 at portal.open-bio.org > Subject: [DAS2] DAS/2 grant meeting at BOSC / ISMB ? > > So we haven't had a big DAS/2 meeting since last September, and I'm > feeling the need for one. I would like to propose we meet during the > upcoming BOSC or ISMB conferences in Detroit (BOSC June 23-24, ISMB June > 25-29). How many of us are already planning to attend one or both of > these conferences? > > Thanks, > Gregg From Gregg_Helt at affymetrix.com Thu May 12 17:07:25 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 12 May 2005 10:07:25 -0700 Subject: [DAS2] imported data into bug tracker Message-ID: I'd also really like to keep bug tracking and feature requests for the spec separate from the client and server implementations. My main reason for this is to emphasize that the spec is entirely independent of the implementations. Too many people I talk to are already confused about the distinction. There should be one spec, but multiple implementations of DAS/2 clients and servers, and not all from the grant collaborators. To me that's an indication that we've succeeded in the primary goal of the grant which is coming up with an improved DAS/2 spec that is widely adopted by the bioinformatics community. The validation suite might be an exception to this distinction. I doubt that anyone else will reimplement this, and I think it's okay for it to be more tightly associated with the spec. gregg > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Chervitz, Steve > Sent: Tuesday, May 10, 2005 3:10 PM > To: Erwin, Ed; das2 at portal.open-bio.org > Subject: Re: [DAS2] imported data into bug tracker > > > Ed Erwin wrote: > > Chervitz, Steve wrote: > >> I thought it might be convenient to use this bugzilla as a one-stop- > shop for > >> tracking all DAS/2 related bugs, including client, server, and > validation > >> suite. > > > > Please do NOT put IGB bugs in the DAS/2 bugzilla, even though it is > > intended to become a DAS/2 client. I already have to keep track of 3 > > bug-reporting repositories for IGB and I don't need a fourth one! > > I also believe it is best to not migrate existing bugs from the > established > client and server bug trackers into the open-bio bugzilla db. > > However, there's a decent chance that people will submit new bugs on the > open-bio bugzilla pertaining to anything related to DAS. Once people start > getting their hands wet with DAS/2, they may naturally gravitate to > bugzilla.open-bio.org, since it is close to biodas.org (in internet space). > > A good solution might be to have a Bugs link on biodas.org pointing to a > page that describes where to go to submit/view bugs for various parts of > DAS/2 that are being developed by the grant: > > * Bugs for the spec -> bugzilla.open-bio.org > * Bugs for the IGB client -> genoviz.sf.net (or where?) > * Bugs for the gmod server -> gmod.sf.net > * Bugs for the validation suite -> ?? > > I can look into setting up this page. > > Steve > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From dalke at dalkescientific.com Thu May 12 17:27:33 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Thu, 12 May 2005 11:27:33 -0600 Subject: [DAS2] imported data into bug tracker In-Reply-To: References: Message-ID: <7abcba93337b0cf722a57c946ad89a0c@dalkescientific.com> Gregg: > The validation suite might be an exception to this distinction. I > doubt > that anyone else will reimplement this, and I think it's okay for it to > be more tightly associated with the spec. Except that I've broken the validation code into two components. One is a das2 Python client and the other is the validator. And people may use the das2 component without using the validator. Andrew dalke at dalkescientific.com From allenday at ucla.edu Thu May 12 17:39:53 2005 From: allenday at ucla.edu (Allen Day) Date: Thu, 12 May 2005 10:39:53 -0700 (PDT) Subject: [DAS2] imported data into bug tracker In-Reply-To: <7abcba93337b0cf722a57c946ad89a0c@dalkescientific.com> References: <7abcba93337b0cf722a57c946ad89a0c@dalkescientific.com> Message-ID: Is there a distiction made between these in CVS, i.e. are they in separate repositories? Have you considered implementing some client components in C? The reason I ask is that I'm interested in having a .so to link to so that I can use a common DAS client API from R, Java, and Perl as well. -Allen On Thu, 12 May 2005, Andrew Dalke wrote: > Gregg: > > The validation suite might be an exception to this distinction. I > > doubt > > that anyone else will reimplement this, and I think it's okay for it to > > be more tightly associated with the spec. > > Except that I've broken the validation code into two components. > One is a das2 Python client and the other is the validator. And > people may use the das2 component without using the validator. > > 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 Thu May 12 17:40:54 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 12 May 2005 10:40:54 -0700 Subject: [DAS2] imported data into bug tracker Message-ID: client++; > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Andrew Dalke > Sent: Thursday, May 12, 2005 10:28 AM > To: DAS/2 > Subject: Re: [DAS2] imported data into bug tracker > > Gregg: > > The validation suite might be an exception to this distinction. I > > doubt > > that anyone else will reimplement this, and I think it's okay for it to > > be more tightly associated with the spec. > > Except that I've broken the validation code into two components. > One is a das2 Python client and the other is the validator. And > people may use the das2 component without using the validator. > > 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 Thu May 12 17:43:46 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 12 May 2005 10:43:46 -0700 Subject: [DAS2] imported data into bug tracker Message-ID: I think the zmap client Ed Griffiths is talking about is going to be implemented in C or C++. Ed? gregg > -----Original Message----- > From: das2-bounces at portal.open-bio.org [mailto:das2-bounces at portal.open- > bio.org] On Behalf Of Allen Day > Sent: Thursday, May 12, 2005 10:40 AM > To: Andrew Dalke > Cc: DAS/2 > Subject: Re: [DAS2] imported data into bug tracker > > Is there a distiction made between these in CVS, i.e. are they in separate > repositories? Have you considered implementing some client components in > C? The reason I ask is that I'm interested in having a .so to link to so > that I can use a common DAS client API from R, Java, and Perl as well. > > -Allen > > On Thu, 12 May 2005, Andrew Dalke wrote: > > > Gregg: > > > The validation suite might be an exception to this distinction. I > > > doubt > > > that anyone else will reimplement this, and I think it's okay for it > to > > > be more tightly associated with the spec. > > > > Except that I've broken the validation code into two components. > > One is a das2 Python client and the other is the validator. And > > people may use the das2 component without using the validator. > > > > 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 edgrif at sanger.ac.uk Thu May 12 18:02:11 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Thu, 12 May 2005 19:02:11 +0100 (BST) Subject: [DAS2] imported data into bug tracker In-Reply-To: References: Message-ID: All, > I think the zmap client Ed Griffiths is talking about is going to be > implemented in C or C++. Ed? The zmap is implemented in C. Most of the code would not be appropriate to be implemented as a .so file but..... zmap (our client) is structured like this: ------ file reader | GUI ----- generalised -----|------ acedb server interface data source | interface | |------ DAS2 server interface | etc the DAS2 server interface could be to a C based parser written as a .so library...we have to write the code to do the parsing so it could potentially form the basis of a DAS2 C parser... I say "potentially" because I would need to think about how much work it would be as we are on a pretty tight schedule for the rest of the work... But a good idea... Ed > > Is there a distiction made between these in CVS, i.e. are they in > separate > > repositories? Have you considered implementing some client components > in > > C? The reason I ask is that I'm interested in having a .so to link to > so > > that I can use a common DAS client API from R, Java, and Perl as well. -- ** PLEASE NOTE NEW ADDRESS/PHONE NUMBER ** ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus | | Hinxton, Cambridge CB10 1HH | | | | email: edgrif at sanger.ac.uk Tel: +44-1223-496844 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From dalke at dalkescientific.com Thu May 12 18:08:39 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Thu, 12 May 2005 12:08:39 -0600 Subject: [DAS2] imported data into bug tracker In-Reply-To: References: <7abcba93337b0cf722a57c946ad89a0c@dalkescientific.com> Message-ID: <2c364bf8bc9867d7a47afb772d2665fa@dalkescientific.com> Allen: > Is there a distiction made between these in CVS, i.e. are they in > separate > repositories? Separate modules, same repository. > Have you considered implementing some client components in > C? The reason I ask is that I'm interested in having a .so to link to > so > that I can use a common DAS client API from R, Java, and Perl as well. No, not at all. That would be hard to do. I'm using some Python specific technologies, like the ElementTree parser to handle XML. I also have rather polymorphic code ("duck typing" at its best) that would be hard to port easily into C. I've found there's a much lower uptake of a given module if it requires a C extension. It's also not covered by the grant. Andrew dalke at dalkescientific.com From dalke at dalkescientific.com Fri May 13 17:40:44 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri, 13 May 2005 11:40:44 -0600 Subject: [DAS2] imported data into bug tracker In-Reply-To: References: Message-ID: <2366abf6bb5fdbab595cb20839328a54@dalkescientific.com> Ed: > the DAS2 server interface could be to a C based parser written as a .so > library...we have to write the code to do the parsing so it could > potentially > form the basis of a DAS2 C parser... Hopefully you'll pull out one of the existing XML parsers instead of writing your own in C. Getting everything right is tricky, from what I understand. Especially when dealing with the various encoding issues (latin-1, utf-8, etc.) You'll end up building your own data types, I assume. Will that include things like a native date/time type or will clients need to parse the ISO string locally? I assume it's passed a string? If not, will it take a FILE *? Or will it be able to do the network connections too? If the latter, how will it work with proxies and other tedious details? If it's just a string then client libraries will still have to do some implementation work. My library will try to fix up known problems, eg, massage the input XML if it comes from a server that's known to have certain bugs. Supporting these in C would be, I think, a lot of work. Though if you used libxml2 and kept the data structure as its DOM and didn't worry about I/O ... Hmmm.... Andrew dalke at dalkescientific.com From Steve_Chervitz at affymetrix.com Fri May 13 18:24:51 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Fri, 13 May 2005 11:24:51 -0700 Subject: [DAS2] hackathon and das2 In-Reply-To: Message-ID: Ed: > > Is there any interest in doing DAS2 stuff at the proposed biohackathon in June > ? The hackathon is being cancelled due to not enough people being able to attend *both* the WWDC and the hackathon, a stipulation of Apple, who also was not able to provide any travel funds. The short notice and the proximity of BOSC just 10 days after it also made things difficult. Apple does have interest in doing something for 2006, but nothing definite yet. > I have someone in my team, Roy Storey, who could come out to work on our > client > (zmap) and making it work with das2. Is anyone else interested/going to this ? > > If people are interested it would be good to know soon as we will need to put > in > travel applications etc. etc. > > > Also, could someone add Roy (rds at sanger.ac.uk) to the das2 mailing list, > thanks. Done. Steve From suzi at fruitfly.org Tue May 17 00:26:00 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Mon, 16 May 2005 17:26:00 -0700 Subject: [DAS2] Fwd: [Fwd: Proposal for subcontract] Message-ID: Gregg (or Steve, or Lincoln) Who is the point person (grant administrator that is) at Affy that manages this? Or is the grant administered from CSH? We have to get moving on this here. I need to introduce our administrator to your administrator. -S Begin forwarded message: > From: Rob Quinlan > Date: May 16, 2005 4:26:37 PM PDT > To: Suzanna Lewis > Cc: Suzanna E Lewis , Nomi Harris > , Sima Misra > Subject: Re: [Fwd: Proposal for subcontract] > > Hello Suzanna, Nomi, & Sima, > > Please provide a name.? An administrative person at the other > institution as a point of contact. > This is somewhat urgent.... you never know what data they will ask > for & we need sufficient time to do it > > Thank you > Rob > ? > > > > Suzanna Lewis wrote: >> Hi Rob, >> >> Thanks for checking in. We are still planning are doing >> this submission. What is the LBL deadline? I've cc-ed >> a couple of other people who will be working with me >> on this, and (importantly) have said that they could help >> with getting you the material you need. I'll still be the >> single point of contact (so your life is easier), but if they >> are included on the exchanges they can be my Jiminy >> Cricket's with getting the material. >> >> -S >> >> On May 15, 2005, at 3:09 PM, Rob Quinlan wrote: >> >>> >>> >>> Have you had a chance to consider your grant submission? I was told >>> it is a subcontract that you are proposing. >>> This is a very busy time for proposals.... I just want to follow up >>> to ensure that you are included in a list we are keeping to handle >>> the excessive number of submissions. >>> >>> Thank you >>> Rob >>> >>> >>> -------- Original Message -------- >>> Subject: >>> Proposal for subcontract >>> Date: >>> Wed, 11 May 2005 15:30:27 -0700 >>> From: >>> Rob quinlan >>> Organization: >>> Lawrence Berkeley National Laboratory >>> To: >>> SELewis at lbl.gov >>> >>> >>> Hi Dr. Lewis: >>> >>> I have been assigned to assist you with your June 15th proposal >>> (subcontract). The internal deadline for an NIH subcontract would be >>> June 7th. >>> >>> In oder to prepare for this, please provide me with the name of the >>> other institution and a point of contact (an administrative person >>> please). Given the excessive workload of this department, it would >>> be >>> great to get ahead of this - so an early reply would be greatly >>> appreciated >>> >>> Thank you >>> Rob Quinlan >>> 495-2506 >>> >>> -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3080 bytes Desc: not available URL: From Gregg_Helt at affymetrix.com Tue May 17 04:56:17 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Mon, 16 May 2005 21:56:17 -0700 Subject: [DAS2] RE: [Fwd: Proposal for subcontract] Message-ID: The point person here at Affymetrix will be Katie Kong (katherine_kong at affymetrix.com), who is the grant administrator here for the current DAS/2 grant. For those of you on the das2 mailing list wondering, what we're talking about is submitting a proposal for continuation of the DAS/2 grant. The continuation would kick in (hopefully) in June 2006 when the current DAS/2 grant is scheduled to expire. gregg -----Original Message----- From: Suzanna Lewis [mailto:suzi at fruitfly.org] Sent: Monday, May 16, 2005 5:26 PM To: Helt,Gregg Cc: Nomi Harris; das2 at portal.open-bio.org; Sima Misra Subject: Fwd: [Fwd: Proposal for subcontract] Gregg (or Steve, or Lincoln) Who is the point person (grant administrator that is) at Affy that manages this? Or is the grant administered from CSH? We have to get moving on this here. I need to introduce our administrator to your administrator. -S Begin forwarded message: From: Rob Quinlan Date: May 16, 2005 4:26:37 PM PDT To: Suzanna Lewis Cc: Suzanna E Lewis , Nomi Harris , Sima Misra Subject: Re: [Fwd: Proposal for subcontract] Hello Suzanna, Nomi, & Sima, Please provide a name. An administrative person at the other institution as a point of contact. This is somewhat urgent.... you never know what data they will ask for & we need sufficient time to do it Thank you Rob Suzanna Lewis wrote: Hi Rob, Thanks for checking in. We are still planning are doing this submission. What is the LBL deadline? I've cc-ed a couple of other people who will be working with me on this, and (importantly) have said that they could help with getting you the material you need. I'll still be the single point of contact (so your life is easier), but if they are included on the exchanges they can be my Jiminy Cricket's with getting the material. -S On May 15, 2005, at 3:09 PM, Rob Quinlan wrote: Have you had a chance to consider your grant submission? I was told it is a subcontract that you are proposing. This is a very busy time for proposals.... I just want to follow up to ensure that you are included in a list we are keeping to handle the excessive number of submissions. Thank you Rob -------- Original Message -------- Subject: Proposal for subcontract Date: Wed, 11 May 2005 15:30:27 -0700 From: Rob quinlan Organization: Lawrence Berkeley National Laboratory To: SELewis at lbl.gov Hi Dr. Lewis: I have been assigned to assist you with your June 15th proposal (subcontract). The internal deadline for an NIH subcontract would be June 7th. In oder to prepare for this, please provide me with the name of the other institution and a point of contact (an administrative person please). Given the excessive workload of this department, it would be great to get ahead of this - so an early reply would be greatly appreciated Thank you Rob Quinlan 495-2506 From Gregg_Helt at affymetrix.com Tue May 17 05:02:25 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Mon, 16 May 2005 22:02:25 -0700 Subject: [DAS2] RE: Fwd: [Fwd: Proposal for subcontract] Message-ID: I've attached the DAS/2 grant proposal (submitted to NIH in February 2003). gregg > -----Original Message----- > From: Nomi Harris [mailto:nomi at fruitfly.org] > Sent: Monday, May 16, 2005 6:29 PM > To: Suzanna Lewis > Cc: Helt,Gregg; Nomi Harris; das2 at portal.open-bio.org; Sima Misra > Subject: Re: Fwd: [Fwd: Proposal for subcontract] > > Another thing we need in order to start writing the grant renewal is a > copy of the original grant application (preferably online rather than > just paper). > Nomi > > On 16 May 2005, Suzanna Lewis wrote: > > Gregg (or Steve, or Lincoln) > > > > Who is the point person (grant administrator that is) > > at Affy that manages this? Or is the grant administered > > from CSH? We have to get moving on this here. I need > > to introduce our administrator to your administrator. > > > > -S -------------- next part -------------- A non-text attachment was scrubbed... Name: Das2GrantFinalB.doc Type: application/msword Size: 355840 bytes Desc: Das2GrantFinalB.doc URL: From suzi at fruitfly.org Tue May 17 17:15:57 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Tue, 17 May 2005 10:15:57 -0700 Subject: [DAS2] Re: [Fwd: Proposal for subcontract] In-Reply-To: References: Message-ID: <0395dda68d0ccd979a082088c1952e2c@fruitfly.org> Thanks Gregg, On May 16, 2005, at 10:02 PM, Helt,Gregg wrote: > I've attached the DAS/2 grant proposal (submitted to NIH in February > 2003). > > gregg > >> -----Original Message----- >> From: Nomi Harris [mailto:nomi at fruitfly.org] >> Sent: Monday, May 16, 2005 6:29 PM >> To: Suzanna Lewis >> Cc: Helt,Gregg; Nomi Harris; das2 at portal.open-bio.org; Sima Misra >> Subject: Re: Fwd: [Fwd: Proposal for subcontract] >> >> Another thing we need in order to start writing the grant renewal is a >> copy of the original grant application (preferably online rather than >> just paper). >> Nomi >> >> On 16 May 2005, Suzanna Lewis wrote: >>> Gregg (or Steve, or Lincoln) >>> >>> Who is the point person (grant administrator that is) >>> at Affy that manages this? Or is the grant administered >>> from CSH? We have to get moving on this here. I need >>> to introduce our administrator to your administrator. >>> >>> -S > > From dalke at dalkescientific.com Tue May 17 18:14:10 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue, 17 May 2005 12:14:10 -0600 Subject: [DAS2] xml and compact formats Message-ID: <1cbb88669b42f0abefdfdc99d680787e@dalkescientific.com> Can someone remind me why we support both XML and "compact" formats? For what I'm doing it complicates things. Was it because of space/verbosity concerns? If so, should we encourage people to use compression on the connections? Andrew dalke at dalkescientific.com From Steve_Chervitz at affymetrix.com Tue May 17 19:10:31 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Tue, 17 May 2005 12:10:31 -0700 Subject: [DAS2] Non-genome DAS templates In-Reply-To: Message-ID: Cool. This adds functionality that goes beyond the scope of the original DAS/2 grant. So we'll have to make it clear that the current spec covers only genome template DAS, but that other templates are possible. This could be an appropriate area to discuss in the DAS/2 renewal. Steve > From: Allen Day > Date: Tue, 17 May 2005 18:39:56 +0000 > To: > Subject: [Gmod-das2-cmts] das2/lib/Bio/Das2/Source/Chado SthCache.pm,1.3,1.4 > > Update of /cvsroot/gmod/das2/lib/Bio/Das2/Source/Chado > In directory > sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23107/lib/Bio/Das2/Source/Chado > > Modified Files: > SthCache.pm > Log Message: > path changes now work. we can implement non-genome das templates now > From allenday at ucla.edu Tue May 17 22:31:00 2005 From: allenday at ucla.edu (Allen Day) Date: Tue, 17 May 2005 15:31:00 -0700 (PDT) Subject: [DAS2] Re: Non-genome DAS templates In-Reply-To: References: Message-ID: yes. as many of you know, i'm implementing a 'matrix' das domain space where you can retrieve the cross product of two other spaces. this is appropriate for, as a concrete example, retrieving a 2-dimensional matrix of measurements of genome features across a series of biological samples (e.g. a microarray). -allen On Tue, 17 May 2005, Chervitz, Steve wrote: > Cool. This adds functionality that goes beyond the scope of the original > DAS/2 grant. So we'll have to make it clear that the current spec covers > only genome template DAS, but that other templates are possible. > > This could be an appropriate area to discuss in the DAS/2 renewal. > > Steve > > > > From: Allen Day > > Date: Tue, 17 May 2005 18:39:56 +0000 > > To: > > Subject: [Gmod-das2-cmts] das2/lib/Bio/Das2/Source/Chado SthCache.pm,1.3,1.4 > > > > Update of /cvsroot/gmod/das2/lib/Bio/Das2/Source/Chado > > In directory > > sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23107/lib/Bio/Das2/Source/Chado > > > > Modified Files: > > SthCache.pm > > Log Message: > > path changes now work. we can implement non-genome das templates now > > > > From suzi at fruitfly.org Wed May 18 18:39:43 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Wed, 18 May 2005 11:39:43 -0700 Subject: [DAS2] DAS/2 grant conf call at 12 PST tomorrow In-Reply-To: References: Message-ID: Hi all, I had dinner with Lincoln last night to discuss the grant and we would like to move tomorrow's call (Thursday May 19) to noon. This is so that Lincoln can make the call. He has group meeting at the earlier time. The other alternative is to have 2 calls. Lincoln really wants to talk with us, Gregg. We also discussed some new aims for the renewal. This would make the existing grant quite a bit larger, but I think that is fine (based on conversations with Peter Good). These are some of the ideas we can talk over tomorrow. 1. Extend specification to include SNP data (contact Steve Sherry at dbSNP) 2. Extend specification to include protein structure data (contact Helen Berman at PDB) 3. Include an analysis server 4. Utilize the established Apollo and GMOD community to form a core of biologists that will actually commit to using DAS2 for the annotation of their organism and the merged apollo-igb (e.g. paramecium?, dictyostelium?) 5. Enable apollo-igb to act as both client and server? 6.... -S From Gregg_Helt at affymetrix.com Wed May 18 19:23:06 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Wed, 18 May 2005 12:23:06 -0700 Subject: [DAS2] RE: DAS/2 grant conf call at 12 PST tomorrow Message-ID: Changing the conference call to noon PST tomorrow sounds good to me. Callin number: USA domestic: 800-531-3250 International: 303-928-2693 Conference ID: 2879055 thanks, gregg > -----Original Message----- > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > Sent: Wednesday, May 18, 2005 11:40 AM > To: Helt,Gregg > Cc: > Subject: DAS/2 grant conf call at 12 PST tomorrow > > Hi all, > > I had dinner with Lincoln last night to discuss the grant > and we would like to move tomorrow's call (Thursday > May 19) to noon. This is so that Lincoln can make the > call. He has group meeting at the earlier time. The other > alternative is to have 2 calls. Lincoln really wants to > talk with us, Gregg. > > We also discussed some new aims for the renewal. > This would make the existing grant quite a bit larger, > but I think that is fine (based on conversations with > Peter Good). These are some of the ideas we can > talk over tomorrow. > > 1. Extend specification to include SNP data > (contact Steve Sherry at dbSNP) > 2. Extend specification to include protein structure data > (contact Helen Berman at PDB) > 3. Include an analysis server > 4. Utilize the established Apollo and GMOD community > to form a core of biologists that will actually commit to > using DAS2 for the annotation of their organism and > the merged apollo-igb > (e.g. paramecium?, dictyostelium?) > 5. Enable apollo-igb to act as both client and server? > 6.... > > -S From lstein at cshl.edu Wed May 18 19:57:04 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Wed, 18 May 2005 15:57:04 -0400 Subject: [DAS2] RE: DAS/2 grant conf call at 12 PST tomorrow In-Reply-To: References: Message-ID: <200505181557.04441.lstein@cshl.edu> Great! Lincoln On Wednesday 18 May 2005 03:23 pm, Helt,Gregg wrote: > Changing the conference call to noon PST tomorrow sounds good to me. > > Callin number: > USA domestic: 800-531-3250 > International: 303-928-2693 > Conference ID: 2879055 > > thanks, > gregg > > > -----Original Message----- > > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > Sent: Wednesday, May 18, 2005 11:40 AM > > To: Helt,Gregg > > Cc: > > Subject: DAS/2 grant conf call at 12 PST tomorrow > > > > Hi all, > > > > I had dinner with Lincoln last night to discuss the grant > > and we would like to move tomorrow's call (Thursday > > May 19) to noon. This is so that Lincoln can make the > > call. He has group meeting at the earlier time. The other > > alternative is to have 2 calls. Lincoln really wants to > > talk with us, Gregg. > > > > We also discussed some new aims for the renewal. > > This would make the existing grant quite a bit larger, > > but I think that is fine (based on conversations with > > Peter Good). These are some of the ideas we can > > talk over tomorrow. > > > > 1. Extend specification to include SNP data > > (contact Steve Sherry at dbSNP) > > 2. Extend specification to include protein structure data > > (contact Helen Berman at PDB) > > 3. Include an analysis server > > 4. Utilize the established Apollo and GMOD community > > to form a core of biologists that will actually commit to > > using DAS2 for the annotation of their organism and > > the merged apollo-igb > > (e.g. paramecium?, dictyostelium?) > > 5. Enable apollo-igb to act as both client and server? > > 6.... > > > > -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 edgrif at sanger.ac.uk Thu May 19 08:09:58 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Thu, 19 May 2005 09:09:58 +0100 (BST) Subject: [DAS2] DAS/2 grant conf call at 12 PST tomorrow In-Reply-To: References: Message-ID: Suzanna, > 4. Utilize the established Apollo and GMOD community > to form a core of biologists that will actually commit to > using DAS2 for the annotation of their organism and > the merged apollo-igb > (e.g. paramecium?, dictyostelium?) Although I'm not part of the grant application I think it would be good to widen this section to include those that don't use Apollo/gmod but could use das2, i.e. sanger, much of which uses acedb based systems of one sort or another. Ed -- ** PLEASE NOTE NEW ADDRESS/PHONE NUMBER ** ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus | | Hinxton, Cambridge CB10 1HH | | | | email: edgrif at sanger.ac.uk Tel: +44-1223-496844 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From Gregg_Helt at affymetrix.com Thu May 19 14:47:56 2005 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Thu, 19 May 2005 07:47:56 -0700 Subject: [DAS2] xml and compact formats Message-ID: For the DAS/2 query for features, I think the ability to support alternative response formats is critical. Yes, this is mainly because of performance issues -- time to generate the XML on the server, time to deliver it over the network, time to parse it and memory footprint on the client side. Standard compression of the XML format is certainly possible, and unless we explicitly forbid it in the spec I see no reason why this can't be declared via the standard Accept-Encoding/Content-Encoding HTTP headers. But consider if network bandwidth is not the bottleneck (for example within an intranet or between sites connected to the Internet2 backbone). Compressing with gzip etc. will actually slow things down, requiring compression on the server and decompression on the client, and not speeding up actual client parsing at all. From experience I can tell you that the decompression cost on the client can be significant. Furthermore, more specific binary formats can be much smaller than compressed das2feature XML. For an extreme example, with an optimized format my client can parse in ~ 1 million SNP annotations per second. And yes, sometimes I need to do that. However, although I think the ability to _support_ alternative feature formats is critical, I don't think we should be declaring a set of alternative feature formats in the specification. We definitely need to have the ability for a server to generate and the client to accept annotation formats that the spec itself knows nothing about. All that is needed is a way for the server to indicate which formats it provides, and the client to choose which one it wants. In the current spec the server indicates which feature formats it supports for a particular versioned source as subelements under a "Feature types" element in the versioned source response. I would like to change this so that the formats supported are specific to the type of feature. This can be done by adding subelements to the elements in the types response. This would allow different alternative formats for different feature types, which I think is necessary -- a format optimized for SNPs is not going to be appropriate for serving up BLAT results, and vice versa. Now as far as the "compact" formats for other (non-feature) responses from the server, I don't think they're necessary. As far as performance issues, the size of these responses are unlikely to be anywhere near as large as the potential responses from a features request. So to summarize, I think the spec definitely needs to support a mechanism for alternative feature formats, but that it should be agnostic as to what those formats are. And I don't think we really need alternative formats for non-feature responses. 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: Tuesday, May 17, 2005 11:14 AM > To: DAS/2 > Subject: [DAS2] xml and compact formats > > Can someone remind me why we support both XML and "compact" > formats? For what I'm doing it complicates things. Was it > because of space/verbosity concerns? If so, should we > encourage people to use compression on the connections? > > Andrew > dalke at dalkescientific.com > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From lstein at cshl.edu Thu May 19 16:44:09 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 19 May 2005 12:44:09 -0400 Subject: [DAS2] xml and compact formats In-Reply-To: References: Message-ID: <200505191244.10215.lstein@cshl.edu> I agree with Gregg on this. There are, for instance, several compact versions of XML that use a binary encoding for each tag and attribute. Lincoln On Thursday 19 May 2005 10:47 am, Helt,Gregg wrote: > For the DAS/2 query for features, I think the ability to support > alternative response formats is critical. Yes, this is mainly because > of performance issues -- time to generate the XML on the server, time to > deliver it over the network, time to parse it and memory footprint on > the client side. > > Standard compression of the XML format is certainly possible, and unless > we explicitly forbid it in the spec I see no reason why this can't be > declared via the standard Accept-Encoding/Content-Encoding HTTP headers. > But consider if network bandwidth is not the bottleneck (for example > within an intranet or between sites connected to the Internet2 > backbone). Compressing with gzip etc. will actually slow things down, > requiring compression on the server and decompression on the client, and > not speeding up actual client parsing at all. From experience I can > tell you that the decompression cost on the client can be significant. > Furthermore, more specific binary formats can be much smaller than > compressed das2feature XML. For an extreme example, with an optimized > format my client can parse in ~ 1 million SNP annotations per second. > And yes, sometimes I need to do that. > > However, although I think the ability to _support_ alternative feature > formats is critical, I don't think we should be declaring a set of > alternative feature formats in the specification. We definitely need to > have the ability for a server to generate and the client to accept > annotation formats that the spec itself knows nothing about. All that > is needed is a way for the server to indicate which formats it provides, > and the client to choose which one it wants. In the current spec the > server indicates which feature formats it supports for a particular > versioned source as subelements under a "Feature types" > element in the versioned source response. I would like to > change this so that the formats supported are specific to the type of > feature. This can be done by adding subelements to the > elements in the types response. This would allow different alternative > formats for different feature types, which I think is necessary -- a > format optimized for SNPs is not going to be appropriate for serving up > BLAT results, and vice versa. > > Now as far as the "compact" formats for other (non-feature) responses > from the server, I don't think they're necessary. As far as performance > issues, the size of these responses are unlikely to be anywhere near as > large as the potential responses from a features request. > > So to summarize, I think the spec definitely needs to support a > mechanism for alternative feature formats, but that it should be > agnostic as to what those formats are. And I don't think we really need > alternative formats for non-feature responses. > > 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: Tuesday, May 17, 2005 11:14 AM > > To: DAS/2 > > Subject: [DAS2] xml and compact formats > > > > Can someone remind me why we support both XML and "compact" > > formats? For what I'm doing it complicates things. Was it > > because of space/verbosity concerns? If so, should we > > encourage people to use compression on the connections? > > > > 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 -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From suzi at fruitfly.org Thu May 19 16:54:21 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Thu, 19 May 2005 09:54:21 -0700 Subject: [DAS2] DAS/2 grant conf call at 12 PST tomorrow In-Reply-To: References: Message-ID: I agree. Mostly want to tap into communities of biologists that would use a DAS in earnest. Any identifiable group we now know of is a good place to start. -S On May 19, 2005, at 1:09 AM, Ed Griffiths wrote: > Suzanna, > > >> 4. Utilize the established Apollo and GMOD community >> to form a core of biologists that will actually commit to >> using DAS2 for the annotation of their organism and >> the merged apollo-igb >> (e.g. paramecium?, dictyostelium?) > > Although I'm not part of the grant application I think it would be > good to widen > this section to include those that don't use Apollo/gmod but could use > das2, > i.e. sanger, much of which uses acedb based systems of one sort or > another. > > > Ed > > -- > ** PLEASE NOTE NEW ADDRESS/PHONE NUMBER ** > > > ----------------------------------------------------------------------- > - > | Ed Griffiths, Acedb development, Informatics Group, > | > | The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus > | > | Hinxton, Cambridge CB10 1HH > | > | > | > | email: edgrif at sanger.ac.uk Tel: +44-1223-496844 Fax: > +44-1223-494919 | > > ----------------------------------------------------------------------- > - From bugzilla-admin-daemon at portal.open-bio.org Thu May 19 16:52:35 2005 From: bugzilla-admin-daemon at portal.open-bio.org (bugzilla-admin-daemon at portal.open-bio.org) Date: Thu, 19 May 2005 12:52:35 -0400 Subject: [DAS2] Bugzilla Change Password Request Message-ID: <200505191652.j4JGqZe4032717@portal.open-bio.org> You (or someone impersonating you) has requested to change your Bugzilla password. To change your password, visit the following link: http://bugzilla.open-bio.org/token.cgi?a=cfmpw&t=DK4i4oah If you are not the person who made this request, or you wish to cancel this request, visit the following link: http://bugzilla.open-bio.org/token.cgi?a=cxlpw&t=DK4i4oah If you do nothing, the request will lapse after 3 days () or when you log in successfully. From dalke at dalkescientific.com Thu May 19 18:45:24 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Thu, 19 May 2005 12:45:24 -0600 Subject: [DAS2] Bugzilla and dasypus status In-Reply-To: <200505191652.j4JGqZe4032717@portal.open-bio.org> References: <200505191652.j4JGqZe4032717@portal.open-bio.org> Message-ID: <123f050e493a506e72e529ea9ea30336@dalkescientific.com> With Steve's help I've set up Bugzilla so that das2 at portal.open-bio.org is the primary owner of all problems. This means people should be able to update the web page and have copies of the changes sent to the mailing list. Except that it looks there's a minor change that needs to be made to Mailman to allow bugzilla-daemon at portal.open-bio.org to send email to the list. I just asked Steve to look at that. If anyone needs it, the Bugzilla password for das2 at portal.open-bio.org is "das2-password" In dasypus I changed the architecture to support different formats for a given request, because that was the spec. (Still needed for the features.) I also worked on code to be able to probe the input stream from the server and change things if there was a problem. Eg, last week's version of the server (haven't checked things this week) didn't emit proper XML. I wanted to be able to patch it and work. Based on my DAS/1 experience I know that that's not uncommon. In the next week I plan to finish off the support for probing and modifying the input stream, and get back to cleaning up the spec based on the various changes in the bug db. Here are the new bugs entered during the last week. 1797 nor P2 All das2 at portal.open-bio.org NEW don't need compact formats for non-feature requests 1798 nor P2 All das2 at portal.open-bio.org NEW add a subelement to for type-specific for... 1799 nor P2 All das2 at portal.open-bio.org NEW server should put server type & version in the HTTP headers 1800 nor P2 All dalke at dalkescientific.com NEW include comment about content-encoding Andrew dalke at dalkescientific.com From Steve_Chervitz at affymetrix.com Thu May 19 18:54:17 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Thu, 19 May 2005 11:54:17 -0700 Subject: [DAS2] Bugzilla and dasypus status In-Reply-To: <123f050e493a506e72e529ea9ea30336@dalkescientific.com> Message-ID: Andrew: > Except that it looks there's a minor change that needs to be > made to Mailman to allow bugzilla-daemon at portal.open-bio.org > to send email to the list. I just asked Steve to look at that. bugzilla-daemon at portal.open-bio.org has been successfully subscribed to DAS2. Steve From allenday at ucla.edu Fri May 20 09:26:31 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 20 May 2005 02:26:31 -0700 (PDT) Subject: [DAS2] RE: DAS/2 grant conf call at 12 PST tomorrow In-Reply-To: <200505181557.04441.lstein@cshl.edu> References: <200505181557.04441.lstein@cshl.edu> Message-ID: Is this a permanent change, or temporary? Is the conference id change permanent or temporary? -Allen On Wed, 18 May 2005, Lincoln Stein wrote: > Great! > > Lincoln > > On Wednesday 18 May 2005 03:23 pm, Helt,Gregg wrote: > > Changing the conference call to noon PST tomorrow sounds good to me. > > > > Callin number: > > USA domestic: 800-531-3250 > > International: 303-928-2693 > > Conference ID: 2879055 > > > > thanks, > > gregg > > > > > -----Original Message----- > > > From: Suzanna Lewis [mailto:suzi at fruitfly.org] > > > Sent: Wednesday, May 18, 2005 11:40 AM > > > To: Helt,Gregg > > > Cc: > > > Subject: DAS/2 grant conf call at 12 PST tomorrow > > > > > > Hi all, > > > > > > I had dinner with Lincoln last night to discuss the grant > > > and we would like to move tomorrow's call (Thursday > > > May 19) to noon. This is so that Lincoln can make the > > > call. He has group meeting at the earlier time. The other > > > alternative is to have 2 calls. Lincoln really wants to > > > talk with us, Gregg. > > > > > > We also discussed some new aims for the renewal. > > > This would make the existing grant quite a bit larger, > > > but I think that is fine (based on conversations with > > > Peter Good). These are some of the ideas we can > > > talk over tomorrow. > > > > > > 1. Extend specification to include SNP data > > > (contact Steve Sherry at dbSNP) > > > 2. Extend specification to include protein structure data > > > (contact Helen Berman at PDB) > > > 3. Include an analysis server > > > 4. Utilize the established Apollo and GMOD community > > > to form a core of biologists that will actually commit to > > > using DAS2 for the annotation of their organism and > > > the merged apollo-igb > > > (e.g. paramecium?, dictyostelium?) > > > 5. Enable apollo-igb to act as both client and server? > > > 6.... > > > > > > -S > > > > _______________________________________________ > > DAS2 mailing list > > DAS2 at portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/das2 > > From Steve_Chervitz at affymetrix.com Sat May 21 01:11:20 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Fri, 20 May 2005 18:11:20 -0700 Subject: [DAS2] Bugzilla and dasypus status In-Reply-To: <123f050e493a506e72e529ea9ea30336@dalkescientific.com> Message-ID: The das2 mailman account for bugzilla was disabled since, apparently, it didn't like receiving the messages it's been getting every time someone posts to the das/2 list: List: DAS2 Member: bugzilla-admin-daemon at portal.open-bio.org Action: Subscription disabled. Reason: Excessive or fatal bounces. I've re-enabled the account and turned off message delivery to this and the bugzilla-daemon account. So it should be back in action, but I haven't tested it. We only need this to be one-way connection: bugzilla sends messages to the das/2 mailman list, not vice versa. Steve > From: Andrew Dalke > Date: Thu, 19 May 2005 12:45:24 -0600 > To: DAS/2 > Subject: [DAS2] Bugzilla and dasypus status > > With Steve's help I've set up Bugzilla so that das2 at portal.open-bio.org > is the primary owner of all problems. This means people should be > able to update the web page and have copies of the changes sent > to the mailing list. > > Except that it looks there's a minor change that needs to be > made to Mailman to allow bugzilla-daemon at portal.open-bio.org > to send email to the list. I just asked Steve to look at that. > > If anyone needs it, the Bugzilla password for das2 at portal.open-bio.org > is "das2-password" > > In dasypus I changed the architecture to support different > formats for a given request, because that was the spec. (Still > needed for the features.) I also worked on code to be able to > probe the input stream from the server and change things if > there was a problem. Eg, last week's version of the server > (haven't checked things this week) didn't emit proper XML. > I wanted to be able to patch it and work. Based on my DAS/1 > experience I know that that's not uncommon. > > In the next week I plan to finish off the support for probing > and modifying the input stream, and get back to cleaning up > the spec based on the various changes in the bug db. > > Here are the new bugs entered during the last week. > > 1797 nor P2 All das2 at portal.open-bio.org NEW don't need compact > formats for non-feature requests > > 1798 nor P2 All das2 at portal.open-bio.org NEW add a subelement > to for type-specific for... > > 1799 nor P2 All das2 at portal.open-bio.org NEW server should put server > type & version in the HTTP headers > > 1800 nor P2 All dalke at dalkescientific.com NEW include comment about > content-encoding > > > 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 Thu May 26 18:29:32 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Thu, 26 May 2005 12:29:32 -0600 Subject: [DAS2] dasypus status Message-ID: <8c9ccda9007b66475af2d280e2b39405@dalkescientific.com> The major client architecture is complete. Finally. It's all in CVS. I started work on updating the spec based on the changes in the bug tracking system, previous discussion, and my experience in implementing the client. I noticed that there was no real introduction or overview section so I started writing that. I would like to merge all of the docs into one. The current split is hard to read because: - one is for the general protocol - one is for GET - one is for writeback - nothing is for general overview/concepts. Keeping it as 3 or 4 pages makes it hard to read, and hard to search. I've started working on the validator proper but it's on hold. Here are some of the warnings generated so far against the prototype server WARNING: Adding X-DAS-Server header 'gmod/0.0' The prototype doesn't mention the DAS server used. I stick one in based on the host name. ERROR: Unknown content-type 'text/x-das-source+xml' for service 'sources' That should be "text/x-das-sources+xml" WARNING: Fixing DAS namespace {http://www.biodas.org/ns/das/2.00}; should be {http://www.biodas.org/ns/das/genome/2.00} WARNING: Fixing base of http://das.biopackages.net:0/das; should be http://das.biopackages.net/das/genome/ ERROR: Unknown content-type 'text/x-das-source-details+xml' for service 'detailed_source' That should be "text/x-das-version+xml", I think. WARNING: VERSION tag not closed There's a bug in the generated XML. Dasypus fixes it. Andrew dalke at dalkescientific.com From bugzilla-daemon at portal.open-bio.org Thu May 26 18:57:30 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 26 May 2005 14:57:30 -0400 Subject: [DAS2] [Bug 1803] New: indicate that two reference coordinate systems are the same Message-ID: <200505261857.j4QIvUYJ014139@portal.open-bio.org> 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. From bugzilla-daemon at portal.open-bio.org Fri May 27 06:20:07 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 27 May 2005 02:20:07 -0400 Subject: [DAS2] [Bug 1807] New: Where do seqids come from? Message-ID: <200505270620.j4R6K71h021749@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1807 Summary: Where do seqids come from? 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 Did a stork drop them off in the cabbage patch? I'm trying to understand regions and their relationship to sequence. The spec says > seqid is the sequence ID, and can correspond to an assembled chromosome, a > contig, a clone, or any other accessionable chunk of sequence Is the seqid exactly equivalent to a region id? I think so given the documentation in das2_protocol.html. The das2_protocol.html document also says > http://server/das/genome/sourceid/version/region/regionid/subregion > A genomic region region identified by the ID of a landmark, modified by > a subregion relative to the landmark. As a whole, the URL is a globally > unique identifier for a region of the genome. > > The syntax of addressing regions and subregions is described in detail later. The das2_get.html document says > Adding a subregion restricts the document further to regions that overlap the indicated subregion. > > REQUEST: > > GET http://server/das/genome/sourceid/version/region/ctg2 > or > GET http://server/das/genome/sourceid/version/region/ctg2/34/128 What are the '24' and '128'? Are they coordinate ranges? Are they independently accessionable chunks of the genome, so that .../sequence/34?format=fasta is valid? Or do I get the sequence via .../sequence/ctg2/34/?format=fasta ------- 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 Fri May 27 06:05:19 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 27 May 2005 02:05:19 -0400 Subject: [DAS2] [Bug 1806] New: When should DAS/2 URLs end with a '/'? Message-ID: <200505270605.j4R65Jwo021604@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1806 Summary: When should DAS/2 URLs end with a '/'? 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 Consider the following http://www.biodas.org/das/genome/human/0/type http://www.biodas.org/das/genome/human/0/region http://www.biodas.org/das/genome/human/0/feature vs. http://www.biodas.org/das/genome/human/0/type/ http://www.biodas.org/das/genome/human/0/region/ http://www.biodas.org/das/genome/human/0/feature/ Which is to be preferred? Should one be required to redirect to the other and if so, which way? I waver between the two. One the one hand, the first grouping makes it easier to understand it when parameters are passed to the URL. .../region?format=agp .../feature?type=exon By comparison, the following looks strange, though legitimate .../region/?format=agp .../feature/?type=exon I did some research on this. One site says http://www.markbaker.ca/2002/01/UriOpacityInvestigation/ ============ The one standout thing about "/" when compared with the other separators, is that has a special meaning in the context of relative and base URI processing. Relative URI are only relative because they are hierarchical. That is, "/wow/gee" is a relative URI, but when grounded to a base URI of; http://example.org/foo/ yields an absolute URI of; http://example.org/foo/wow/gee This suggests that URI publishers should be concerned about whether their URI end in "/" or not. If the URI might ever be used as a container, it should end with "/". This also suggests that the relationship between a URI with a terminating slash, and the same URI without the terminating slash, is also nothing more than that same non-specific hierarchical relationship. ============= In that case we should be using '/' for most of the URLs. A problem comes in with subregions to a region. When does a subregion name end with a '/'? Eg, if the following exists (assuming there are no children under 128) .../region/ctg2/34/128 then what about .../region/ctg2 ? On a system with writeback support will someone ever be able to create a sub-part? I assume not. Similarly, the following would not be appropriate .../sequence/Contig2 because there's always the chance of selecting a range from it .../sequence/Contig2/1000:2000 This is an ambiguity in the PUT spec as well. Consider one lock request section which specifies filter_href="feature?overlaps=Chr3/1000:500000" and another which specifies POST http://dev.wormbase.org/das/genome/volvox/1/feature/?lock=xyzzy My current belief is: - all of the namespaces ("sequence/", "region/", "feature/", ...) must end with a "/". This means we will have URLs like .../region/ChrX/?format=das2xml .../feature/?type=exon - the assembly will not change for a given version so we specify that anything with a subregion must be referenced with a '/' and the server must redirect names that are missing the '/'. Terminal regions must not end with a '/'. - Terminals (the actual feature, lock, etc.) must not end with a '/'. The odd one out is the .../sequence/ namespace. Is .../sequence/Contig1 ever allowed, given that clients may use .../sequence/Contig1/200:350 ? Note, btw, that sequence/ ranges are one of the few parts of the DAS spec which is not REST-ful, because it violates the idea that URLs are opaque to the client, excepting for '?' query parameters. ------- 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 Fri May 27 06:25:22 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 27 May 2005 02:25:22 -0400 Subject: [DAS2] [Bug 1808] New: , region ids and sequence ids Message-ID: <200505270625.j4R6PMMK021838@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1808 Summary: , region ids and sequence ids 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 In bug 1807 I asked how region ids are related to sequence ids. I think they are supposed to be the same, so to get the sequence for a given region you append the region id to the sequence namespace. How does the client know which namespace to use? I think it's supposed to be hard-coded into the client that "/sequence/" contains the genomic DNA. Otherwise there is insufficient information in the versioned source request to figure out which URL to use. Consider this example from the spec There's not enough information for the client to figure out that the "volvox/1/sequence" URL contains genomic sequences while the "volvox/1/protein" contains protein sequences. I would rather have a 'type' field where the type data is from a well-defined vocabulary. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee.