[DAS2] paper? was: Re: Notes from the biweekly DAS/2 teleconference, 2 Apr 2007

Ann Loraine aloraine at gmail.com
Mon Apr 2 18:19:27 UTC 2007

Dear all,

Sorry I didn't come to the meeting today!

I just  wanted to ask about the DAS2 paper. The BioMoby group are
working on a draft, and it seems to be near finishing. If you are at
the proper stage for it, it would be terrific if the DAS2 project
could be published soon, since the two projects have similarities. I
expect that if the two papers came out at about the same time, some
"buzz" could be generated over bioinformatics Web services, which I
expect would be great for both projects. Also, it would be good to
explain how the two approaches are complementary, and not competing.
If people think the two are doing the same thing, then support would
be harder to get.

btw, the BioMoby draft is under version control in the BioMoby cvs
repository. It might be good to take a look.

All the best!


On 4/2/07, Steve Chervitz <Steve_Chervitz at affymetrix.com> wrote:
> Notes from the biweekly DAS/2 teleconference, 2 Apr 2007
> $Id: das2-teleconf-2007-04-02.txt,v 1.1 2007/04/02 17:36:32 sac Exp $
> Teleconference Info:
>    * Schedule:         Biweekly on Monday
>    * Time of Day:      9:30 AM PST, 17:30 GMT
>    * Dialin (US):      800-531-3250
>    * Dialin (Intl):    303-928-2693
>    * Toll-free UK:     08 00 40 49 467
>    * Toll-free France: 08 00 907 839
>    * Conference ID:    2879055
>    * Passcode:         1365
> Attendees:
>     Affy: Steve Chervitz, Ed Erwin, Gregg Helt
>     UCLA: Brian O'connor
> Note taker: Steve Chervitz
> Action items are flagged with '[A]'.
> The teleconference schedule and links to past minutes are now
> available from the Community Portal section of the biodas.org site:
> http://www.biodas.org/wiki/BioDAS:Community_Portal
> Meeting notes are checked into the biodas.org CVS repository at
> das/das2/notes/. Instructions on how to access the DAS/2 CVS
> repository are at http://www.biodas.org/wiki/DAS/2#CVS_Access
> The note taker aims for completeness and accuracy, but these goals are
> not always achievable, given the desire to get the notes out with a
> rapid turnaround. So don't consider these notes as complete minutes
> from the meeting, but rather abbreviated, summarized versions of what
> was discussed. There may be errors of commission and omission.
> Participants are welcome to post comments and/or corrections to these
> as they see fit.
> Agenda
> -------
> * General stuff
> * Status reports
> Topic: General Stuff
> --------------------
> gh: Andrew Dalke and I met a week ago in Bay area, talked about
> das1->das2 proxy. He'll be in UK in 4 wks to visit with Sanger, and
> Andreas to get the proxy going at the DAS/2 registry. I also spoke
> with Andreas over phone. Still wants to do work, but juggling
> priorities.
> Status Reports
> --------------
> ee: this is my last week on this call (moving to new project at
> Affy). Lots of work trying to finish things up for igb and das/2
> grant. Developed style sheet system for use in igb, v0.1. It works,
> not sure if well enough for the das/2 spec, but we might consider
> using it as a basis for the das/2 spec. it's an xml style sheet,
> cascading, app-specific, user-specific, doc-specific with rules of
> precedence. independent of data format, so it will work regardless of
> where data came from (das2xml or gff3 or else). can specify styles for
> things that have multiple levels of hierarchy (mrna->exons->
> etc.). Not as completely finished as I'd have liked, but a decent start.
> ee: Other things I did: focused on igb as a client. Users specifying prefs
> in igb w/o editing files, but via gui now. Future work: will be
> documenting things i have done, but not much more development of new
> features.
> gh: there will be a new igb release in 2-weeks. I will take over
> release cycle. stylesheet stuff should play nice with the 5-level
> stuff for affy data that Steve has been working with (exon/gene array). you
> can say: "these things here, although they are children of this, you display
> them outside. you can display two different things in the same track.
> ee: can display children outside of their parent, or have multiple
> displays for a single thing.
> gh: I worked on getting better graph support into das2 server and igb
> to do graphs (plots) in das2. it's there on server side, indexing data
> and serving it up efficiently. client is working. now just a matter of
> installing.  other stuff: tricks to better organize types, better than
> a flat list of annotation types, but more as a tree. First set of
> experiments will have 50 different annotation types (e.g., cell
> lines).  Doing this outside of the das protocol itself, as a
> convention in type names to be path names. Builds a tree where each
> node in path
> E.g.,:   geneprediction/genescan
>          geneprediction/geneid
>          ...
> Will create a node for geneprediction, you can then collapse/expand it
> in the UI. Trouble: Using tabletree component, and there's no good
> impl in Java swing for this yet.
> ee: not based on ontology?
> gh: no. looking at the SO (sequence ontology), my use case is, how do
> you split off gene predictions from alignments, etc. It doesn't say
> "predicted transcript" for example. There's no way in SO to
> differentiate something based on gene prediction from something that
> has been experimentally observed. I'm just doing this as a convention
> for now to see how it works. we can revisit doing it as an ontology.
> gh: also am working on adding better feat filter support on the affy
> das/2 server. also am working on draft of das/2 paper to get it out
> before end of grant. Should be able to extend the grant beyond the end
> of May and end of june given current burn rate.
> sc: very busy past few weeks on Affy-related work: Netaffx annotation
> update and new product support (Human Gene array "HuGene"). Added
> support to Affy public das servers for the new array, das/1 and
> das/2. Plan to be working on configuring the new replacement machine
> for the Affy das public server this week and next. Primary focus is
> setting up a local mirror for the data that is on the public machine.
> gh: Space requirements for mirroring the affy public server data must
> account for adding tiling graph data, (40-60 G).
> gh: have you looked into the maximum RAM per java thread on the new
> machine?
> sc: no. am thinking now that having multiple threads segregated by
> technology type (ivt, exon, gene, etc.) will be better. This way, we
> won't have to take down the whole server just to fix or add data for
> one array.
> gh: ok, as long as we can make it look like it's all coming from the
> same server url.
> sc: shouldn't be a problem with url rewriting.
> [NOTE: the following was added after teleconference:
> sc: I did some work on the biodas.org site adding teleconference
> schedule and links to meeting minutes (see 'Community Portal'
> page). Also added entry for genome annotation to wikiomics.org site
> and created reciprocal links to/from biodas.org. See
> the first sentence of the biodas.org main page for the link. Also
> added link from wikipedia page to wikiomics.org site, see
> http://en.wikipedia.org/wiki/Genome_annotation#Genome_annotation
> ]
> bo: last week I filed - so am completely done with degree. yay! next
> two weeks can dedicate to helping Allen Day with revision of das/2
> server. He can assign me tasks. Will know more after meeting with him
> tomorrow.
> gh: writeback?
> bo: not sure. he said he made lots of progress on revision of
> server. He'll assign me things on his todo list, bugracker. getting it
> packaged up out the door. postdocing in a second lab to finish
> projects/papers for ~6 mos. next report will have more to say.
> gh: let me know if things need to happen in igb to set status of
> writeback, e.g.
> Wrapup
> -------
> Next meeting: 16 April 2007
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> DAS2 at lists.open-bio.org
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Ann Loraine, Assistant Professor
Departments of Genetics, Biostatistics,
Computer and Information Sciences
Associate Scientist, Comprehensive Cancer Center
University of Alabama at Birmingham

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