http://www.mailbucket.org MailBucket http://www.mailbucket.org/nexml_discuss-6449530.html Rutger et. al -- did any consensus on ID-handling come out from the last day of the working group meeting? -Aaron ]]> Fri, 23 May 2008 11:57:46 -0400 http://www.mailbucket.org/nexml_discuss-6449530.html http://www.mailbucket.org/nexml_discuss-6433451.html Hi all, we're just wrapping up the third EvoInfo meeting at NESCent, so here are some of the significant happenings: * nexml i/o implementations are growing in number: Dave Swofford has started implementing it in paup, Xuhua Xia demonstrated it fully formed in DAMBE, Aaron Mackey has started it for R's phylobase package, Weigang Qiu has started it for BioPerl. * Enrico Pontelli has started mapping the character data analysis ontology (CDAO, http://evolutionaryontology.org) onto the nexml schema. * Jim Leebens-Mack wants to endorse nexml in MIAPA (the "minimal reporting standards" recommendation for phylogenetic analyses). * Jim Ballhoff is debating whether to implement it in phenote (http://www.phenote.org) * mesquite now reads and writes nexml, including dictionary attachments and IDs. * we're debating whether to organize a nexml-specific hackathon at some point. * we're debating which data resources/services to hassle about nexml i/o (e.g. what about CIPRES? TreeBaseII? Those sorts of things). * we're debating where to get funding to guarantee continuity of development. All in all, things are moving. Cheers, Rutger -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Thu, 22 May 2008 17:02:27 -0400 http://www.mailbucket.org/nexml_discuss-6433451.html http://www.mailbucket.org/nexml_discuss-4693671.html Hi, the svn restructuring is complete. The structure is now according to svn conventions: nexml/trunk/nexml (was nexml/) nexml/tags (would be used for tagged releases) nexml/branches/ (now has a branch substitution-models/, within which is folded the contents of the "experimental" folder, with substitution model code) Everything seems sane, the build process on the webserver is functioning as expected. Rutger -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Wed, 6 Feb 2008 23:40:11 -0800 http://www.mailbucket.org/nexml_discuss-4693671.html http://www.mailbucket.org/nexml_discuss-4689747.html Hi guys, I'd like to do the svn directory change tonight, so please do any pending commits by the end of the day! Cheers, Rutger -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Wed, 6 Feb 2008 14:04:59 -0800 http://www.mailbucket.org/nexml_discuss-4689747.html http://www.mailbucket.org/nexml_discuss-4631212.html I posted this as an feature request, but the html got screwed up (or rather, did not get honored) ... Here is another suggested syntax for representation of multi-states. Main difference is that instead of allowing an in-place nested definition of uncertain states within a polymorphic state element, we restrict child elements of both the uncertain and polymorphic state to "member" elements, each of which must reference a previously defined state. To refer to an ambiguous state, we define it first, and then refer to it by its id. -- jeet ------------------------------- Jeet Sukumaran ------------------------------- Division of Herpetology Department of Ecology and Evolutionary Biology / Natural History Museum and Biodiversity Research Center University of Kansas Dyche Hall 1345 Jayhawk Blvd Lawrence KS 66045-7561 ------------------------------- Phone: 785-864-3439 Fax: 785-864-5335 E-mail(s): jeet@ku.edu, [message truncated] -- ------------------------------- Jeet Sukumaran ------------------------------- Division of Herpetology Department of Ecology and Evolutionary Biology / Natural History Museum and Biodiversity Research Center University of Kansas Dyche Hall 1345 Jayhawk Blvd Lawrence KS 66045-7561 ------------------------------- Phone: 785-864-3439 Fax: 785-864-5335 E-mail(s): jeet@ku.edu, jeetsukumaran@frogweb.org ------------------------------- KU Herpetology: http://nhm.ku.edu/herpetology/ Frogs of the Malay Peninsula: http://frogweb.org HerpWatch Philippines: http://www.herpwatch.org/ Photograph Galleries: http://www.jeetworks.com/ ------------------------------- ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Fri, 01 Feb 2008 18:22:35 -0600 http://www.mailbucket.org/nexml_discuss-4631212.html http://www.mailbucket.org/nexml_discuss-4613470.html Hi all, Can I get some clarification on the parsing of standard characters marked up as sequences? From the schema, it appears that this is only allowed if the characters are represented as a string of space-delimited integers ... is this correct? If so, then what do these integers represent? The schema suggests a "StandardToken", but this attribute definition is commented out of the definition of a StandardState. So how do these integers map to state definitions? Another alternative is to restrict standard character mark-up to single character-length symbols in sequence notation; if multi-character symbols are desired or needed, then cell-by-cell mark-up should be used. -- jeet ------------------------------- Jeet Sukumaran ------------------------------- Division of Herpetology Department of Ecology and Evolutionary Biology / Natural History Museum and Biodiversity Research Center University of Kansas Dyche Hall 1345 Jayhawk Blvd Lawrence KS 66045-7561 ------------------------------- Phone: 785-864-3439 Fax: 785-864-5335 E-mail(s): jeet@ku.edu, jeetsukumaran@frogweb.org ------------------------------- KU Herpetology: http://nhm.ku.edu/herpetology/ Frogs of the Malay Peninsula: http://frogweb.org HerpWatch Philippines: http://www.herpwatch.org/ Photograph Galleries: http://www.jeetworks.com/ ------------------------------- ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Thu, 31 Jan 2008 12:00:29 -0600 http://www.mailbucket.org/nexml_discuss-4613470.html http://www.mailbucket.org/nexml_discuss-4577878.html Hi all, Peter, Mark, Jeet and I just came out of a skype telecon. Here are the topics we discussed. For the participants, please note that I added some more explanations that I couldn't come up with in the call, so this might be worth reading: * We had some discussion about the "char" element and attribute. Character matrices in the verbose, categorical case are marked up as follows: first a "format" element, which encloses one or more state set definitions (for example, a state set for different dental arrangements, a state set for litter sizes, etc.), then a sequence of "char" elements (i.e. columns in a matrix) that each define what state set they use, then the "matrix" element, in which each cell in a row defines, through attributes whose values are ID references, what column ("char") it belongs to, and what state it occupies. One question was whether the "char" attribute - and by extension the element it refers to - could be renamed "col" (or "column"). This seems to be somewhat of a matter of taste, though one might argue (and Rutger did) that it makes sense for an observation in a character state matrix to specify what character and what state it refers to - as opposed to what column and what state. On the other hand, a matrix consists of rows and columns, so perhaps it makes sense, instead, for each cell in a row in a matrix to specify its column. (The latter would require renaming, which would then have to propagate into various parser libraries, so a slight PITA). A related issue is that in some other concrete subclasses - specifically, all granular molecular matrices - the "char" attribute's value is a non-negative integer - i.e. not an ID reference but a column number - so that these matrices don't require column definitions (which would usually be lengthy for molecular sequences) just to resolve the coordinates of cells in a sparse matrix. This looks like a vote for "column" instead of "char". The polling stations are now open to declare your passionate preference for a renaming of "char" to "col/column". * Why does AbstractChar inherit from Labelled even though it has an ID attribute (so maybe it should inherit from IDTagged)? The rationale is as follows: cells in granular molecular matrices have a char attribute that is a non-negative integer, the column number. However, in the general case, that char attribute refers to an explicitly declared char element (not a column implied by an index). Hence, for consistency's sake, that ID attribute on the AbstractChar element should also be allowed to be an integer, to accommodate both implicit columns in large matrices where we don't care to declare every column in a sequence alignment as well as explicit column definitions about which we might have more to say - but xml ID's are traditionally (i.e. in DTDs as opposed to schemas) not allowed to be integers, and because the nexml schema should follow xml idioms the ID attributes of the superclass IDTagged are of type xs:NCName (=strings, not integers). Because inheritance in xml schema works such that you cannot inherit from IDTagged but then change the type of the ID attribute from string to integer for this special case I needed instead to inherit from Labelled, then re-implement the ID attribute in such a way that in some character subclasses it is a string, and in others an integer (which is why in the superclass its type is xs:anySimpleType, to allow for both derivations). There's a number of ways to resolve this special casing: 1. make all nexml ID attributes integers. This means they are no longer strictly speaking XML id's, which would preclude them from being used as such in, for example, xpath expressions, relative URLs, etc. This is not an attractive option because it diverges from assumptions made by people and xml toolkits, and w3c recommendations. 2. NEVER have column definitions in granular molecular matrices, so that the "char" attribute in cells of these subclasses are column numbers, but not (also) references to pre-declared column definitions. This means that anything that is assumed to be constant across all rows for a given column (and therefore most sensibly placed in a column definition, e.g. codon position, tRNA secondary structure) has to be repeated across all rows. 3. ALWAYS have column definitions with standard ID's (strings), so that the "char" attribute is a conventional ID reference, not an integer. This means increased verbosity. For example, for a Cytochrome B alignment you would have a sequence of 1140 elements that go char id="c1" .. char id="c1140" within the format element. However, if we have anything more useful to say about each column this solution quickly becomes less verbose than 2. 4. Leave as is, so that the "char" attribute is both a column number, and (optionally) a reference to a column definition that has an ID attribute whose value is an integer. * a question about the MSTokenLength type, which would be instantiated as the value of a "token Long message truncated by MailBucket.]]> Mon, 28 Jan 2008 15:39:50 -0800 http://www.mailbucket.org/nexml_discuss-4577878.html http://www.mailbucket.org/nexml_discuss-4576197.html Hi, my skype name is rutgeravos talk to you soon, Rutger -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Mon, 28 Jan 2008 12:55:16 -0800 http://www.mailbucket.org/nexml_discuss-4576197.html http://www.mailbucket.org/nexml_discuss-4573743.html Hi Wayne, Sorry that that time will not work for you. This week is crazy here (we are in the midst of 2 searches, and I am teaching a class for the first time...). Rutger indicated that he could call in, so perhaps Peter, Jeet, Rutger and I can talk. After you and Rutger confer we could schedule a follow-up to clear up issues that you feel strongly about. Cheers, Mark On Jan 28, 2008, at 10:55 AM, Wayne Maddison wrote: > FWIW, I teach 1-4 today PST > Wayne > > At 3:36 PM -0600 25.1.2008, Mark Holder wrote: >> Sorry. >> >> Could we chat 3:00 (Central time) on Monday? >> >> Cheers, >> Mark >> >> >> Mark Holder >> >> mtholder@ku.edu >> http://www.people.ku.edu/ >> ~mtholder/ >> >> ============================================== >> Department of Ecology and Evolutionary Biology >> University of Kansas >> 6031 Haworth Hall >> 1200 Sunnyside Avenue >> Lawrence, Kansas 66045 >> >> lab phone: 785.864.5789 >> alt. phone: 785.371.4666 >> >> fax (shared): 785.864.5860 >> ============================================== >> >> >> >> >> >> >> >> --------------------------------------------------------------------- >> ---- >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> >> _______________________________________________ >> Nexml-discuss mailing list >> Nexml-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/nexml-discuss > > > -- > -------------------------------------------------------- > Wayne Maddison > Professor and Canada Research Chair > Depts. of Zoology and Botany and > Biodiversity Research Centre > & Director > Beaty Biodiversity Museum > 6270 University Boulevard > University of British Columbia > Vancouver, BC V6T 1Z4 Canada > > email: wmaddisn@interchange.ubc.ca FAX: (604) 822-2416 > > Mesquite: http://mesquiteproject.org > MacClade: http://macclade.org > Salticidae: http://salticidae.org > Tree of Life: http://tolweb.org > Beaty Biodiversity Museum: http://biodiversity.ubc.ca/museum > Home page: http://salticidae.org/wpm/home.html Mark Holder mtholder@ku.edu http://www.people.ku.edu/~mtholder/ ============================================== Department of Ecology and Evolutionary Biology University of Kansas 6031 Haworth Hall 1200 Sunnyside Avenue Lawrence, Kansas 66045 lab phone: 785.864.5789 alt. phone: 785.371.4666 fax (shared): 785.864.5860 ============================================== ]]> Mon, 28 Jan 2008 11:30:05 -0600 http://www.mailbucket.org/nexml_discuss-4573743.html http://www.mailbucket.org/nexml_discuss-4573344.html FWIW, I teach 1-4 today PST Wayne At 3:36 PM -0600 25.1.2008, Mark Holder wrote: >Sorry. > >Could we chat 3:00 (Central time) on Monday? > >Cheers, >Mark > > >Mark Holder > >mtholder@ku.edu >http://www.people.ku.edu/~mtholder/ > >============================================== >Department of Ecology and Evolutionary Biology >University of Kansas >6031 Haworth Hall >1200 Sunnyside Avenue >Lawrence, Kansas 66045 > >lab phone: 785.864.5789 >alt. phone: 785.371.4666 > >fax (shared): 785.864.5860 >============================================== > > > > > > > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >_______________________________________________ >Nexml-discuss mailing list >Nexml-discuss@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/nexml-discuss -- -------------------------------------------------------- Wayne Maddison Professor and Canada Research Chair Depts. of Zoology and Botany and Biodiversity Research Centre & Director Beaty Biodiversity Museum 6270 University Boulevard University of British Columbia Vancouver, BC V6T 1Z4 Canada email: wmaddisn@interchange.ubc.ca FAX: (604) 822-2416 Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Salticidae: http://salticidae.org Tree of Life: http://tolweb.org Beaty Biodiversity Museum: http://biodiversity.ubc.ca/museum Home page: http://salticidae.org/wpm/home.html ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Mon, 28 Jan 2008 08:55:03 -0800 http://www.mailbucket.org/nexml_discuss-4573344.html http://www.mailbucket.org/nexml_discuss-4544894.html Sorry. Could we chat 3:00 (Central time) on Monday? Cheers, Mark Mark Holder mtholder@ku.edu http://www.people.ku.edu/~mtholder/ ============================================== Department of Ecology and Evolutionary Biology University of Kansas 6031 Haworth Hall 1200 Sunnyside Avenue Lawrence, Kansas 66045 lab phone: 785.864.5789 alt. phone: 785.371.4666 fax (shared): 785.864.5860 ============================================== ]]> Fri, 25 Jan 2008 15:36:32 -0600 http://www.mailbucket.org/nexml_discuss-4544894.html http://www.mailbucket.org/nexml_discuss-4544877.html We have a few questions about the , MSTokenLength and StandardChar element. Could we chat next Monday at 2:00PM Central Time? Cheers, Mark Mark Holder mtholder@ku.edu http://www.people.ku.edu/~mtholder/ ============================================== Department of Ecology and Evolutionary Biology University of Kansas 6031 Haworth Hall 1200 Sunnyside Avenue Lawrence, Kansas 66045 lab phone: 785.864.5789 alt. phone: 785.371.4666 fax (shared): 785.864.5860 ============================================== ]]> Fri, 25 Jan 2008 15:35:16 -0600 http://www.mailbucket.org/nexml_discuss-4544877.html http://www.mailbucket.org/nexml_discuss-4219781.html Hi Jeet, The xsi:schemaLocation attribute is intended to associate a namespace (the first part of the attribute's value) with a path to a schema file. The first bit in this case is http://www.nexml.org/1.0, which is the namespace for nexml, the second part can be a relative path (relative to the instance document), an absolute path or an url to a schema file. Relative to the /nexml/examples folder, the path within the source tree to the root schema file is ../xsd/nexml.xsd, so the first one is correct. Perhaps even better would be to start using the url for the schemaLocation, so that you'd get: xsi:schemaLocation="http://www.nexml.org/1.0 http://www.nexml.org/1.0/nexml.xsd" Cheers, Rutger On Dec 28, 2007 8:57 PM, Jeet Sukumaran wrote: > > Rutger: > > In some of the example files, the schema location is given as: > > xsi:schemaLocation="http://www.nexml.org/1.0 ../xsd/nexml.xsd" > > Should this not be: > > xsi:schemaLocation="http://www.nexml.org/1.0 nexml.xsd"? > > Not sure if it matters, one way or another, as both pass validation. > > > -- jeet > > > ------------------------------- > Jeet Sukumaran > ------------------------------- > Division of Herpetology > Department of Ecology and > Evolutionary Biology / > Natural History Museum and > Biodiversity Research Center > University of Kansas > Dyche Hall > 1345 Jayhawk Blvd > Lawrence KS 66045-7561 > ------------------------------- > Phone: 785-864-3439 > Fax: 785-864-5335 > E-mail(s): jeet@ku.edu, > jeetsukumaran@frogweb.org > ------------------------------- > KU Herpetology: > http://nhm.ku.edu/herpetology/ > Frogs of the Malay Peninsula: > http://frogweb.org > HerpWatch Philippines: > http://www.herpwatch.org/ > Photograph Galleries: > http://www.jeetworks.com/ > http://jeet.smugmug.com/ > ------------------------------- > > -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Sat, 29 Dec 2007 02:14:16 +0100 http://www.mailbucket.org/nexml_discuss-4219781.html http://www.mailbucket.org/nexml_discuss-4217145.html Rutger: In some of the example files, the schema location is given as: xsi:schemaLocation="http://www.nexml.org/1.0 ../xsd/nexml.xsd" Should this not be: xsi:schemaLocation="http://www.nexml.org/1.0 nexml.xsd"? Not sure if it matters, one way or another, as both pass validation. -- jeet ------------------------------- Jeet Sukumaran ------------------------------- Division of Herpetology Department of Ecology and Evolutionary Biology / Natural History Museum and Biodiversity Research Center University of Kansas Dyche Hall 1345 Jayhawk Blvd Lawrence KS 66045-7561 ------------------------------- Phone: 785-864-3439 Fax: 785-864-5335 E-mail(s): jeet@ku.edu, jeetsukumaran@frogweb.org ------------------------------- KU Herpetology: http://nhm.ku.edu/herpetology/ Frogs of the Malay Peninsula: http://frogweb.org HerpWatch Philippines: http://www.herpwatch.org/ Photograph Galleries: http://www.jeetworks.com/ http://jeet.smugmug.com/ ------------------------------- ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Fri, 28 Dec 2007 13:57:37 -0600 http://www.mailbucket.org/nexml_discuss-4217145.html http://www.mailbucket.org/nexml_discuss-4215457.html Hi, this week in nexml history: * I sent Bill Piel and Tobias Thierer (of geneious fame) updates on nexml progress over the last months, and our plans up till May 2008. Both expressed interest, with Bill mentioning he would request SDSC implement nexml serialization of TreeBaseII output. Tobias looked at our code in a little more detail, became interested in the xml beans and complained he couldn't find their sources or an easy to find link to the svn repository. I made the nexmlbeans sources available in the downloads section, and updated the info for the svn feed * Jeet has been expanding the python bindings, adding tests and logging facilities. * Boris Kolpackov of CodeSynthesis has provided a driver program that parses nexml files (with particular focus on characters blocks in the example) using bindings generated from the schema. Driver code, a makefile and a build script are now in /nexml/cpp, bindings are available in the downloads section. For an idea of what nexml processing in C++ using these bindings feels like, look at http://www.nexml.org/nexml/cpp/driver.cxx * The schema has been cleaned up somewhat: unused schema files are now all in /nexml/experimental, file inclusions (which turned out to be a problem for generated c++ code) have been broken. Best wishes, Rutger -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Fri, 28 Dec 2007 18:19:48 +0100 http://www.mailbucket.org/nexml_discuss-4215457.html http://www.mailbucket.org/nexml_discuss-4148500.html Hi, thanks for the conference call, I think that was quite effective. To summarize what we talked about, here are the goals for the working period up to May 2008: * prepare manuscript. We agreed this would be a latex document in a subsection of the svn repository, that we might start by copying and pasting from the wiki, then edit collaboratively in our working copies. The remainder of the todo list consists of things that would have to be done to make this manuscript exciting. * clean up schema, move "extensions" (i.e. things that we'd like to have but don't require changes to core elements) to a separate branch, for version 1.1 * create "canonical" examples, both to refer to in the manuscript and for various testing suites * implement parsers or bindings in 5 languages: java, c++, python, perl, ( ruby | js ) * implement support in 5 applications or toolkits: Mesquite, BioPerl, HyPhy, R, pynexml/BioPython. Other options include: NCL, JEBL, BioRuby * implement support in 3 online services: nexus=>nexml converter (Mesquite in TomCat), Tree of Life, TreeBaseII, (CIPRES, pPod, Morph(o)bank?) That's a fairly ambitious (but not impossible) list which requires some division of labor. I realize nexml is currently a project that doesn't justify deferring things that are "shot-at-dawn" urgent (teaching, publishing, reviewing, writing proposals, etc. etc.) so anything you can volunteer for would be wonderful, but by no means expected. Okay, here's the list of things I would need help with: * C++ support. The download section has generated CodeSynthesis/XSD compliant bindings: http://nexml-dev.nescent.org/nexml/downloads/cpp-bindings.tar.gz - can anyone play around with these to see if they are useful? * Python support. It would be great of pynexml became compatible with "the" python bioinformatics/phyloinformatics toolkit. Whether that's BioPython, and what that would entail, I don't know. * Several things are pushed onto Mesquite. Hopefully, Wayne, Peter and I can come up with some division of labor that include: "web service" capabilities (can Mesquite run in TomCat?), Mesquite R bridge for nexml IO, expansion/improvement of nexml support. * Apache xmlbeans. The website has a "nexmlbeans.jar" for download. These are plain vanilla xmlbeans generated using Apache's scomp tool. Can anyone play around with them to see if they're useful? * More writing: example files, source documentation, manuscript. * More "outreach": I just emailed Val Tannen and Bill Piel, but we may need more proselytizing in the direction of other web services (or really anyone who might be interested). It would be great if some momentum would form and nexml would become more community-driven. Happy holidays! Rutger -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Fri, 21 Dec 2007 16:35:22 -0800 http://www.mailbucket.org/nexml_discuss-4148500.html http://www.mailbucket.org/nexml_discuss-4146624.html Still very much work in progress, but here they are: http://nexml-dev.nescent.org/xsd-3.0.0-i686-macosx/bin/out/ -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Fri, 21 Dec 2007 12:50:58 -0800 http://www.mailbucket.org/nexml_discuss-4146624.html http://www.mailbucket.org/nexml_discuss-4146451.html Hi, the consensus on the mailing list has indicated that we call in at 1pm PST, i.e. in half an hour. I prefer using skype (rutgeravos) as I don't have teleconferencing infrastructure - but maybe Team Kansas does? In that case, my phone number is +1 604 780 0190 Rutger -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Fri, 21 Dec 2007 12:29:20 -0800 http://www.mailbucket.org/nexml_discuss-4146451.html http://www.mailbucket.org/nexml_discuss-4141035.html Okay, Friday at 1:00PM PST / 3:00 CST: telecon. On Dec 20, 2007 5:14 PM, Peter E. Midford wrote: > Tomorrow at 3:00 sounds good to me. > > Peter > > On Dec 19, 2007, at 15:48, Rutger Vos wrote: > > > So: how about Friday at 1:00PM PST / 3:00 CST? I'm in. > > > > Rutger > > > > ------------------------------------------------------------------------- > > SF.Net email is sponsored by: > > Check out the new SourceForge.net Marketplace. > > It's the best place to buy or sell services > > for just about anything Open Source. > > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > > _______________________________________________ > > Nexml-discuss mailing list > > Nexml-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/nexml-discuss > > -- > Peter Midford > Mesquite Developer > > > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > _______________________________________________ > Nexml-discuss mailing list > Nexml-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/nexml-discuss > -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Fri, 21 Dec 2007 04:10:19 -0800 http://www.mailbucket.org/nexml_discuss-4141035.html http://www.mailbucket.org/nexml_discuss-4136540.html Tomorrow at 3:00 sounds good to me. Peter On Dec 19, 2007, at 15:48, Rutger Vos wrote: > So: how about Friday at 1:00PM PST / 3:00 CST? I'm in. > > Rutger > > ------------------------------------------------------------------------- > SF.Net email is sponsored by: > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services > for just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > _______________________________________________ > Nexml-discuss mailing list > Nexml-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/nexml-discuss -- Peter Midford Mesquite Developer ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Nexml-discuss mailing list Nexml-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nexml-discuss ]]> Thu, 20 Dec 2007 19:14:20 -0600 http://www.mailbucket.org/nexml_discuss-4136540.html