January 2010 GMOD Meeting

January 2010 GMOD Meeting January 14-15, 2010 Following PAG 2010 San Diego, California, USA

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The next GMOD community meeting will be held January 14-15, 2010, in San Diego, immediately following Plant and Animal Genome XVIII (PAG 2010). The meeting will be held at the Best Western Seven Seas (see Lodging below), which is adjacent to the Town and Country Resort, where PAG is being held.

The meeting is now full. However, you may get on the waiting list by filling out the registration form now.

Thanks to the generous support of USDA-ARS and NIH, registration for this meeting is free. Special thanks to Scott Markel and Accelrys for providing meeting equipment for us to use.

Guest Speaker: Dr. Maryann Martone Professor, UC San Diego Principal Investigator, Neuroscience Information Framework (NIF) Co-Director, National Center for Microscopy and Imaging Research (NCMIR)

Our special guest speaker will be Dr. Maryann Martone, who will discuss her work on using ontologies in the field of neuroscience. Her research demonstrates the power of ontologies to bring together large volumes of disparate data into a unified whole using the semantic relationships that ontologies enable. Maryann is a Professor at UC San Diego, where she is the PI for the Neuroscience Information Framework (NIF), a web portal, providing simultaneous, deep web searches across multiple databases, web pages and literature. She is also Co-Director of the National Center for Microscopy and Imaging Research (NCMIR), where her research focuses on ontologies in image analysis and data mining tools.

Agenda Proposals

If you have something you want to be on the agenda at this meeting please add it below.

• Using the 2009 GMOD Community Survey results for guidance -- Dave Clements
• 2010 GMOD Summer Schools -- Dave Clements
• GMOD tools in the frame of GnpAnnot projects (-- Michael Alaux -- Joelle Amselem, on the 14th)
  • Roundtrip GBrowse ← Chado ↔ Apollo at URGI for community of annotation (fungal and plant genomes)
  • The Chado Controller : a user authentication and logging addon to Chado.
  • GMOD Report : a Java based middleware for Chado.
• Using and developing Schema, integrating it with other DBIx::Class-based code -- Robert Buels
• Discussion toward standard website platforms for MOD sites -- Robert Buels
• StrategiesWDK: intro to a powerful MOD-compatible search UI -- Steve Fischer
• Give Textpresso meeting talk, Nathan Liles
• TableEdit, Daniel Renfro, Jim Hu, TableEdit on MediaWiki
• Providing a biologist-centered interface for running and customizing Ergatis pipelines -- Chris Hemmerich
• Using Drupal and Flex to Create User-Configurable Interfaces for GMOD Databases for Use in Transcriptional Genomics Research -- Michael Caudy
• Discussion/BoF for Hadoop & HBase. Our lab is starting to store next gen sequence data in HBase and I would be interested in talking with others interested building and deploying large genome database using these technologies. -- Brian O'Connor
• Your suggestion here. (Login to edit this section.)

Satellite Meetings

This year (for the first time I believe) there will be satellite meetings in addition to the main meeting. Satellite meetings are about a particular topic or work area of interest that people want to spend more time on then they can during the main meeting.

• Satellite meetings re self-organized. That is, if you want to get together with other people to discuss or work on a particular topic:
  • Suggest a satellite meeting below, and on the appropriate GMOD Mailing Lists.
  • Include your contact information and a suggested time and date.
  • You may also want to create a wiki page for the satellite meeting.
• Satellite meetings take place outside the times of the main meeting.
• Satellite meetings have any particular space reserved for them. As the meetings crystallize, the GMOD Help Desk will be happy to help locate nearby facilities with free wifi.

Topic	Suggested Date	Organizer(s)	Comments
GMOD REST Hackathon	January 13, all day, starting at 9am	Josh Goodman (email)	I'd like to do a small GMOD REST API hackathon with a goal of producing a working prototype at the end. Ideally I'd like to do a solid day of coding activities but if you can only come for part of thetime that is fine too. I've posted a rough schedule and other information on the GMOD REST Hackathon page. If you want to attend please add your name to that page.
BioPerl	January 13, all day, starting at 11:30am	Jason Stajich, Chris Fields	This will be a meeting (possibly followed by a hackathon) that will address BioPerl's current issues, future directions, etc. It is anticipated that there will be overlap with other groups and satellite meetings. Sign up for the meeting and detail specific topics on the main BioPerl website.
Tripal Working Group	January 13, 4-6pm	Stephen Ficklin	A discussion of Tripal with an emphasis on future development plans. Anyone using Tripal, planning on or interested in it, or with an interest in using Drupal as a web front end to Chado is encouraged to attend. If you are interested, please add your name to the Tripal Working Group page. You may also want to subscribe to the Tripal mailing list.
Chado Natural Diversity Module Working Group	January 8, 5pm	Dave Clements	A discussion of the Chado Natural Diversity Module, currently under development. If you are interested, please add your name to the working group page (once that page exists :-).

Agenda

The final agenda will be posted shortly before the meeting. Please don't make changes to the agenda below without clearing it with Scott first (yes, I know it's a wiki ...)

Thursday, January 14

Time	Topic	Presenter(s)	Links
10:00*	Introductions and the State of GMOD	Scott Cain	PDF
11:00	Report from the Help Desk	Dave Clements	PPT, PDF
11:30	Brief status updates: Projects, satellite meetings, etc	You
12:30	Lunch (catered on site)
1:30	GMOD tools in the frame of GnpAnnot projects	Michael Alaux and Joelle Amselem	PDF
2:15	StrategiesWDK: intro to a powerful MOD-compatible search UI	Steve Fischer	StrategiesWDK, PPT, PDF
2:45	Chado on Rails (Ruby on Rails and Chado)	Justin Reese, Chris Childers	Slides on Google Docs, PPT, PDF
3:15	Coffee Break
3:30	Using and developing Schema, integrating it with other DBIx::Class-based code	Robert Buels	PPT, PDF
4:00	Using Drupal and Flex to Create User-Configurable Interfaces for GMOD Databases for Use in Transcriptional Genomics Research	Michael Caudy	PPT, PDF
4:30	Discussion toward standard website platforms for MOD sites
5:00	Dinner (on your own)

*Yes, we start at 10:00am on Thursday; the meeting room is unavailable before then.

Friday, January 15

Time	Topic	Presenter(s)	Links
9:00	Textpresso	Nathan Liles	PPT, PDF
9:30	TableEdit	Daniel Renfro, Jim Hu	PPT, PDF
10:00	Adventures in NOSQL	Brian O'Connor, SeqWare	ODP, PDF
10:30	Coffee break
10:45	The Neuroscience Information Framework: Establishing a practical semantic framework for neuroscience	Maryann Martone	PPT, PDF
11:30	NCBO Tools and Web Services	Trish Whetzel	PPT, PDF
12:00	Lunch
1:15	Providing a biologist-centered interface for running and customizing Ergatis pipelines	Chris Hemmerich	PPT, PDF
1:45	Open Mic/Show and Tell: JBrowse non-model marker discovery update on BGD, BeeBase, NasoniaBase Tripal Use of GBrowse 1.999 in the Cancer Genome Project Next Gen Seq - Mainly 'look it works', warnings about what not to use as the Human reference COSMIC - Catalogue Of Somatic Mutations In Cancer - DAS/GFF3 as public resource GFF3 issues. 'Nice to have' features. TopoView GBrowse glyph at FlyBase others	You

Meeting Participants

First Name(s)	Last Name	Affiliation	URL
Michael	Alaux	INRA, France	http://urgi.versailles.inra.fr/
Joelle	Amselem	INRA-URGI	http://urgi.versailles.inra.fr/
David	Arcoleo	Institute for Genomic Biology, University of Illinois, Urbana-Champaign	http://beespace.uiuc.edu
Yuri	Bendana	USC BISC-MCB
Aaron	Buechlein	The Center for Genomics and Bioinformatics
Robert	Buels	SGN	http://solgenomics.net
Scott	Cain	GMOD / OICR	http://gmod.org / http://www.oicr.on.ca/
Michael	Caudy	Reactome	http://www.reactome.org
Chris	Childers	Bovine Genome Database; BeeBase; NasoniaBase; Hymenoptera Genome Database	http://bovinegenome.org; http://beebase.org; http://nasoniabase.org; http://hymenopteragenome.org
Dave	Clements	GMOD / NESCent	http://gmod.org / http://nescent.org
Jonathan	Crabtree	Institute for Genome Sciences / University of Maryland Baltimore
Stephen	Ficklin	Clemson University Genomics Institute	http://www.genome.clemson.edu/
Christopher	Fields	BioPerl, Institute for Genomic Biology	http://bioperl.org http://beespace.igb.uiuc.edu
steve	fischer	EuPathDB	http://EuPathDB.org
Eric	Ganko	Syngenta
Aureliano Bombarely	Gomez	Boyce Thompson Institute for Plant Research	http://solgenomics.net/
Josh	Goodman	FlyBase	http://flybase.org/
Chris	Hemmerich	Center for Genomics and Bioinformatics	http://cgb.indiana.edu/
LE, Quang	Hien	Vilmorin & Cie	http://www.vilmorin.info
Ben	Hitz	SGD	http://www.yeastgenome.org/
Zhiliang	Hu	Iowa State University	http://www.animalgenome.org
Jim	Hu	EcoliWiki	http://ecoliwiki.net
Juan	Jovel	Scripps
John	Lee	USDA-ARS-WRRC-GGD
Nathan	Liles	Textpresso / GBrowse / EcoliWiki	http://textpresso.org
Dawei	Lin	UC Davis	http://bioinformatics.ucdavis.edu/
Maryann	Martone	UC San Diego	Neuroscience Information Framework (NIF), National Center for Microscopy and Imaging Research (NCMIR)
Sheldon	McKay	CSHL/iPlant	http://mckay.cshl.edu, http://iptol.iplantcollaborative.org
Rex	Nelson	SoyBase	http://soybase.org
Brian	O'Connor	GMODWeb
Youlian	Pan	National Research Council Canada, Ottawa / Arabidopsis / Brassica	http://www.nrc-cnrc.gc.ca/iit-iti/index.html
Ram	Podicheti	Center for Genomics and Bioinformatics	http://www.cgb.indiana.edu/
Keiran	Raine	Cancer Genome Project (Wellcome Trust) - Human, Mouse	http://www.sanger.ac.uk/research/projects/cancergenome.html
Justin	Reese	BeeBase/Bovine Genome Database/Hymenoptera Genome Database
Daniel	Renfro	EcoliWiki	http://ecoliwiki.net
Lacey-Anne	Sanderson	Dept Plant Sciences, University of Saskachewan
Carl	Schmidt	University of Delaware / Gallus
Mitchell	Skinner	UC Berkeley	http://jbrowse.org
Richard	Smith	University of Cambridge	http://www.intermine.org
Jason	Stajich	BioPerl, FungalGenomes, University of California, Riverside	http://fungalgenomes.org/
Meg	Staton	Clemson University Genomics Institute	Tripal http://www.fagaceae.org http://www.rosaceae.org
Jaideep	Sundaram	Computational Genomics Laboratory Georgetown University
Alexander	Tchourbanov	New Mexico State University, Biology Department	http://www.wyomingbioinformatics.org/~achurban/
Maxim	Troukhan	Ceres, Inc.
Trish	Whetzel	NCBO
Eric Kenneth	Wafula	Depamphilis Lab, Penn State university	http://depcla4.bio.psu.edu/

Venue and Lodging

The meeting is being held at the Best Western Seven Seas, which is adjacent to the Town and Country Resort, where PAG is being held. Rooms are available to GMOD meeting participants at the special rate of $72/night plus tax. Rooms can be booked at this rate for the entire duration of PAG 2010 and this GMOD meeting. The hotel also offers a complimentary shuttle to and from the airport.

A room can be booked by calling +1 619 291 1300. Mention "GMOD" to get the special rate.

Feedback

Please provide feedback on this meeting.

Feedback on previous meetings has been very helpful to the organizers:

• August 2009
• January 2009
• 2008 and before