January 2010 GMOD Meeting

From GMOD
Revision as of 19:55, 26 January 2010 by Clements (Talk | contribs)

Jump to: navigation, search
Jan2010MtgLogo170.png
January 2010 GMOD Meeting
January 14-15, 2010

Following PAG 2010
San Diego, California, USA
{{#icon: SanDiegoConvention.gif|San Diego Convention and Visitors Bureau http://www.sandiego.org/nav/Visitors}}

__NOTITLE__

This GMOD community meeting was held January 14-15, 2010, in San Diego, immediately following Plant and Animal Genome XVIII (PAG 2010). This meeting was full. Thanks to the generous support of USDA-ARS and NIH, registration for this meeting was free. Special thanks to Scott Markel and Accelrys for providing meeting equipment for us to use.

Satellite Meetings

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

Topic Organizer(s) Comments
GMOD REST Hackathon 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.

BioPerl 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 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 Dave Clements A discussion of the Chado Natural Diversity Module, currently under development.

Agenda

http://login.ncmir.ucsd.edu/Contact/Personnel/maryann_Martone.htm}}
 
Guest Speaker: Dr. Maryann Martone

Our special guest speaker was Dr. Maryann Martone, who discussed her work using ontologies in the field of neuroscience. Her research demonstrated 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.

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: Satellite Meetings
GMOD REST Hackathon
Josh Goodman GMOD RPC API
BioPerl
Jason Stajich, Chris Fields
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 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 HTML
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)

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, ZIP
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
Mitch Skinner PDF
Openings at SGD
Ben Hitz
Connecting high-throughput data with hypotheses
Dawei Lin
Tripal
Stephen Ficklin (PAG 2010 Talk)
Use of GBrowse 1.999 in the Cancer Genome Project
Keiran Raine PPT, PDF
TopoView GBrowse glyph at FlyBase
Josh Goodman PDF
Ceres Genome Browser
Maxim Troukhan
InterMine
Richard Smith HTML, PDF,
A Couple of UI Prototypes
Jonathan Crabtree OpenOffice, PDF
WebGBrowse
Ram Podicheti
5:30 Finish

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 http://bovinegenome.org; http://beebase.org; http://nasoniabase.org; http://hymenopteragenome.org
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/

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 GBrowseChadoApollo 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.)



Best Western Seven Seas

Venue and Lodging

The meeting was held at the Best Western Seven Seas, which is adjacent to the Town and Country Resort, where PAG is being held.

Feedback

Please provide feedback on this meeting.

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