January 2010 GMOD Meeting

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


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.


Maryann Martone
Guest Speaker: Dr. Maryann Martone

The Neuroscience Information Framework: Establishing a practical semantic framework for neuroscience (PPT, PDF, ZIP)

Our guest speaker was Dr. Maryann Martone, who discussed her work using ontologies in 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
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 Bio::Chado::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
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
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
Mitch Skinner PDF
Openings at SGD
Ben Hitz
RediscoveryDB: Connecting High-Throughput Data with Testable Hypotheses
Dawei Lin PDF
PhaseolusGenes : A Genomics Information Management and Marker Discovery Toolkit For A Non-Model Organism
Dawei Lin PDF
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
Richard Smith HTML, PDF,
A Couple of UI Prototypes
Jonathan Crabtree OpenOffice, PDF
Ram Podicheti
5:30 Finish

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.

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
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 Bio::Chado::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.


Attendees were asked to provide feedback at the end of the meeting.

Q: Would you recommend GMOD meetings to others

Yes Maybe No
95% 5% 0%

The maybe response was:

very technical so only to the right audience

Q: Please rate the meeting(s) using the following scale: 1 (not at all) to 3 (reasonably) to 5 (exceptionally).

1 2 3 4 5
How useful was the meeting? 5% 0% 19% 38% 38%
Was the meeting well run and organized? 5% 0% 0% 47% 47%

The "1" rating for both these questions came from the same person. However, that person was absolutely positive on all other questions. So, it's possible they didn't pay attention to if 1 was good or if 5 was good.

Q: Was the meeting what you expected?

No. Yes. Other
5% 90% 5%

Longer responses:

  • No, but that was a good thing. Informal atmosphere was great, felt much more comfortable asking questions. -- the "no" response
  • would have liked a little more discussion of what is new in gbrowse 2.0 -- the "other" response
  • Yes, I expected a lot of technical discussion about projects, and I had a number of ideas for improvement of our system.
  • Yes, and it beat my expectations. I was expecting to hear about Gbrowse and Jbrowse but I also learned about Chado, data integration, NoSQL and ontologies.
  • More than I expected.

Q: Which presentations and sessions at this meeting were the most useful or interesting?

  • Update/overview of all GMOD projects (helps for Scott to run through all of them)
  • StrategiesWDK was great but it was unclear how to integrate this in generic format to other projects.
  • Introductions and the State of GMOD
  • StrategiesWDK: intro to a powerful MOD-compatible search UI Steve Fischer StrategiesWDK, Using Drupal and Flex to Create User-Configurable Interfaces for GMOD Databases for Use in Transcriptional Genomics Research
  • StrategiesWDK - saw this a something that could be used in our system, TableEdit - Nice to see something of a completely generic nature which simplifies something we all hate, NCBO - Did not know about this, we have a tissue ontology system which can be added, Ergatis - Appears to be an excellent system, may be able to implement internally with some extensions... future contribution?
  • REST Hackathon, Strategies SDK, Open Mic session, Chado on Rails, * JBrowse, NoSQL
  • StrategiesWDK: intro to a powerful MOD-compatible search UI, Chado on Rails, Using and developing Bio::Chado::Schema, integrating it with other DBIx::Class-based code, The Neuroscience Information Framework: Establishing a practical semantic framework for neuroscience, JBrowse
  • StrategiesWDK: intro to a powerful MOD-compatible search UI
  • Rob Buell's Bio::Chado::Schema
  • The NIF keynote presentation, Bio::Chado::Schema, StrategiesWDK, Status updates/help desk"
  • gnpAnnot, Ergatis pipeline, StrategiesWDK
  • Steve Fischer's query trees demo was intriuging - it's a great way for user to dive into the data, TopoView GBrowse glyph at FlyBase - very cool, The Ergatis demo was interesting, but seems too complicated to use elsewhere.
  • The data integration presentations (InterMine, Strategies) were very useful, since I hadn't seen these before. The Drupal/Flex was also interesting and well as the Ergatis pipeline tool. The Chado related ones were good since I wasn't that familiar with Chado. This has motivated me to install Chado/PostgreSQL and get to know them better and possibly use it for phenotype data. The NoSQL talk was good too because I haven't heard much about distributed db. I liked The NIF talk since I haven't had much exposure to ontologies. I also liked the final afternoon where people can go up and give demos.
  • O'Conner (NOSQL), Caudy (Drupal), Martone (NIF), Skinner (JBrowse), in general talks that describe GMOD tools briefly, to orient us to what they do"
  • Using and developing Bio::Chado::Schema, GnpAnnot projects, Chado on Rails
  • JBrowse, bioperl & DBIx, tripal, show and tell
  • Representation of next generation sequences in GBrowse.
  • The "current state of GMOD" presentations by Scott Cain, Dave Clements were very useful, as were the later updates on the release status of what you might call the core GMOD components (e.g., chado, GBrowse and also Mitchell's talk on JBrowse.) I liked Michael Alaux's presentation on the Chado Controller because it was an example of coming up with a general solution to a problem that other people might be able to use too. I thought Brian O'Connor's "Adventures in NOSQL" was great because in 15 minutes he presented a bunch of useful information that it would take me hours to compile on my own. Dr. Martone's invited talk was also excellent and very impressive and I thought the open mic session was also a great idea.
  • TableEdit by Daniel Renfro, Jim Hu, Tripal by Stephen Ficklin

Q: Do you have suggestions for improving GMOD meetings in the future?

  • Target a session on a particular topic -- ie comparative genomics, or visualization, or data integration and queries. Focusing on how collaborative solutions can also be generated from the various projects so there is good level of communication.
  • I like the free discussion style, but probably a little more time control would be better.
  • Better WiFi or wired network connections
  • Better time keeping. I think it is great to have a relaxed meeting but there should be some effort to keep talks close to the allocated time. I would prefer more time for the Open Mic, probably with a definite time limit on each. I was interested in the MODs using common web interface session which we never got to.
  • Having a larger meeting may be helpful. Its great to see the broad range of topics. Many of them provide great ideas.
  • The show-and-tell talks went a bit long. A bit more structure limiting time would be great.
  • Perhaps a time for asking advice - I have this problem, or we use this setup. This happened on an ad hoc basis and was some of the more useful bits from the conference.
  • I think some of the demos ran long, maybe have a 15 min time limit.
  • humbly suggest that you consider enforcing time limits on talks, or with small grace periods. some seemed to go on too long. this would give latecomers on the agenda more time.
  • Set up schedule in advance and uploading presentations a few days before the meeting for participants to have a chance to dig into what is to be presented.
  • Limit show and tells to a reasonable amount of time (which will clearly be ignored, but the thought counts )
  • Make it bigger by not limiting the number of participants.
  • Definitely keep the open mic session but impose a strict (and short) time limit.
  • If possible, to have the complete presentation agenda earlier.

Additional feedback, suggestions, criticism, and praise.

  • Interoperability needs to be emphasized for some of the sets of disparate projects. Length, location, and timing was appropriate - tying the meeting to other conferences is a good thing. Consider genome informatics as well even if that is just an update meeting rather than a full blown 2-3 day affair.
  • Thanks, well done
  • I would most likely attend any meeting held in Europe if this was to go ahead as suggested.
  • The Satellite meetings should happen again, adding a special interest day makes the travel more worthwhile.
  • Wonderful job. Thanks for a great meeting.
  • a little more enforcement of time limits would be a good idea!
  • Thank you for a very well organized and informative meeting. It was a pleasure interacting over lunch and dinner as well with the other attendees. This allowed me to make a contact which will be helpful in completing a task in my job. Since I work alone on my project, it's very helpful to interact with other bioinformaticians.
  • Thanks for building the GMOD software, it makes life much easier.
  • Good meeting, and it's great that all the slides/presentations are going to be available online. Thanks!

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