March 2011 GMOD Meeting

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This GMOD community meeting was held March 5-6 2011, at NESCent in Durham, North Carolina, as part of GMOD Americas 2011, which also included Satellite Meetings, and a GMOD Course.

For the first time, the meeting was preceded by a GMOD Overview session the night before. This session was intended to help GMOD newcomers (of which there are usually many) learn the big picture in GMOD and get the most out of the meeting that follows.

This meeting was hosted and sponsored by NESCent.

GMOD Meetings are a mix of user and developer presentations, and are a great place to find out what is happening in the project, what's coming up, and what others are doing.

The next meeting will be held in October 2011 at the Ontario Institute for Cancer Research (OICR) in Toronto, Canada. OICR is the current home of both GBrowse and BioMart.


About GMOD

GMOD is the Generic Model Organism Database project, a collection of interoperable open-source software components for annotating, visualizing, managing and analyzing biological data. GMOD is also an active community of software developers and biologists addressing common challenges with their data.

The GMOD suite includes widely used tools such as GBrowse and JBrowse (and WebGBrowse) for genome browsing, Apollo and MAKER for genome annotation, GBrowse_syn and CMap for comparative genomics visualization, Chado, BioMart and InterMine for data integration, management, and querying, and Galaxy and Ergatis (and ISGA) for data analysis.

Registration

The registration fee for the March 2011 GMOD Meeting was

  • $80 on or before February 18
  • $95 after February 18

The Satellite Meetings were free and were attended by over 20 people.

GMOD Americas Events

The schedule of events is below. This is subject to slight revisions.

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Date Time Event
Friday
March 4
7pm-9pm Introduction to GMOD
An overview of the GMOD project for GMOD newcomers, the night before the meeting starts. If you are new to GMOD this will give you the background you need to get the most out of the Community Meeting.
Saturday
March 5
9am-5pm GMOD Community Meeting
Talks and discussions on GMOD Components, project direction and planning, best practices, recent developments, extensions, ...

See Agenda and Agenda Proposals for details.

Sunday
March 6
9am-5pm
Monday
March 7
8:30am-5pm Satellite Meetings
GMOD special interest groups and birds-of-a-feather meetings where GMOD community members can discuss topics of common interest.

If you are attending the Community Meeting, you are strongly encouraged to also attend a Satellite Meeting as well.

Tue-Sat
March 8-12
All Day 2011 GMOD Spring Training
A week long hands-on course on GMOD Component installation, configuration, and usage. The course will cover these components in detail:

ApolloMAKERGBrowseChadoInterMineJBrowseGBrowse_synTripalGalaxy

Agenda

Eric Stone

Guest Speaker: Dr. Eric Stone

Assistant Professor of Genetics and Statistics
Bioinformatics Research Center
North Carolina State University

Our guest speaker was Dr. Eric Stone of North Carolina State University. Eric will speak on his experience with the Drosophila Genetic Reference Panel (DGRP), a project using 192 inbred lines to detect "polymorphisms (SNPs and indels) with a minor allele frequency of 0.02 or greater." A project with the scope of the DGRP poses unique challenges in areas that GMOD focuses on. Eric discussed the scope of the project, the types of data being generated, some of the scientific goals, and community needs and solutions with respect to visualization, data management, annotation, and providing useful and informative access to that much data. As sequencing prices continue to drop, many GMOD users may be doing similarly large projects in the not too distant future.


Friday: Introduction to GMOD

This session the night before the meting gave an introduction to the GMOD project, community, and components. It gave GMOD newcomers a clearer picture of the project in advance of the meeting.

Time Topic Presenter(s) Links
7pm-9m Introduction to GMOD Scott Cain

Saturday: Day 1

Time Topic Presenter(s) Links
9:15 Introductions Scott Cain
9:35 Welcome to NESCent, & opportunities at the center Todd Vision slides
9:50 The State of GMOD Scott Cain PPT
10:35 Coffee
10:50 GMOD Help Desk Update Dave Clements PPT
11:55 Lunch
1:15 Drosophila Genetic Reference Panel (DGRP) Eric Stone
2:00 GSA and GMOD Elizabeth Ruedi PPT
2:30 Coffee
3:00 Mashing up InterMine: An introduction to the new InterMine webservice features Alex Kalderimis Slides?
3:45 Mimosa: Miniature Model Organism Sequence Aligner Jonathan "Duke" Leto Slides
4:30 Head out for dinner

Sunday: Day 2

This agenda will be finalized prior to the meeting. In the meantime, please see the confirmed speakers list.

Time Topic Presenter(s) Links
9:15 JBrowse Project Update Mitch Skinner Slides
10:00 Tripal Project Update Lacey Sanderson Slides
10:45 Break
11:10 Galaxy for high-throughput sequence data analysis Dave Clements
12:00 Lunch
1:00 Implementation of RNA-Seq data in Chado at FlyBase Dave Emmert Slides
2:00 Lightning talks:
Ergatis
Chris Hemmerich
ISGA
Chris Hemmerich
Coffee break
Modware: Its latest development using Moose and Bio::Chado::Schema
Siddhartha Basu PPT, Slideshare
Developing genome sequencing for identification, detection, and control of Bactrocera dorsalis (Hendel) and other Tephritid pests
Tom Walk PPT
Genome Synteny Viewer
Kashi Ravenna PPT

Monday: Satellite Meetings

GMOD Americas 2011 continued on Monday with partial and full day Satellite Meetings.

Participants

First Last Affiliation
Siddhartha Basu Northwestern university
Robert Buels Sol Genomics Network - Boyce Thompson Institute
Scott Cain Ontario Institute for Cancer Research (OICR), GMOD
Dave Clements Emory University, Galaxy
James Collett Pacific Northwest National Laboratory
David Emmert FlyBase - Harvard University
Madhavan Ganesh University of California, Berkeley
Eric Ganko Syngenta Biotech
Steve Graham Syngenta
Christopher Hemmerich Center for Genomics and Bioinformatics
Joe Horton GSK
Alex Kalderimis University of Cambridge, FlyMine, InterMine
Jonathan Leto Sol Genomics Network - Boyce Thompson Institute
Zhanji Liu Delaware State University
Olaf Mueller Duke University
Trevor Newell Delaware State University
Daniel Quest Oak Ridge National Lab (JGI)
Kashi Revanna UNT
Elizabeth Ruedi Genetics Society of America (GSA)
Victor Ruotti Morgridge Institute for Research
Surya Saha Cornell University
Lacey-anne Sanderson University of Saskatchewan
Sheena Scroggins Polytechnic of NYU
Mitchell Skinner UC Berkeley
Olen Sluder Texas Biomedical Research Institute
Tomasz Smolinski Delaware State University
Eric Stone North Carolina State University
Yaqoob Thurston Delaware State University
Todd Vision NESCent
Tom Walk USDA ARS
Gary xie LANL

Help Get the Word Out

Help spread the word about GMOD Americas 2011 events by posting and distributing this flier, or the event announcements to your communities, mailing lists, and organizations.

There are many organizations out there that are struggling to cope with the volume of data that they have and will continue to get in the future. GMOD provides excellent options for helping these groups get a grip on and exploit their data.

GMOD Americas 2011 Flier

Logistics

See the GMOD Americas 2011 page for information on lodging, transportation and meals.

Feedback

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%

"Maybe" Response:

  • Yes for newcomers, those with new developments that are relevant, and for those looking for potential help/collaboration


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? 0% 0% 5% 33% 62%
Was the meeting well run and organized? 0% 0% 14% 38% 48%


Q: Was the meeting what you expected?

No Somewhat Yes Other
5% 9% 86% 0%

Longer responses:

  • Yes, the crowd is always a bit of a surprise, but having so many new and prospective users made for a very interactive session.
  • yes- good to hear about new developments and network with others
  • Yes and more then i expected.
  • Yes, and much more!
  • Yes: I came into the meeting hoping to learn about the software, but also to understand the community. Mission accomplished!
  • it exceeded my expectations in terms of relevance to my current job.
  • First meeting but more than expected. Nescent is a great location to foster discussion.
  • Yes, absolutely. I will attend again. It is one of the most productive meetings of the year for me.
  • Yes. I really appreciated the efforts that were made to get us to gether and talk about not only technical but also the anthropological issues in the development and adoption of open source bioinformatics software.
  • In part, but there was a surprising lack of discussion of GMOD-wide issues (e.g. component integration, user support, next steps, etc), which concerned me.
  • No, it was better!

Note: Next time, we should reword this question to: Did the meeting meet your expectations? (possible answers: Exceed, Met, Almost, No, and an explanation box.


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

  • Tripal update.
  • DGRP, Galaxy, RNAseq in Chado
  • GMOD state, JBrowse, Tripal, Galaxy
  • Ergatis, Tripal, Galaxy
  • The state of gmod
  • Intermine * Mimosa * keynote (Drosophila) * RNA-seq data at Flybase
  • Intro session was great to get a background of the GMOD project. Eric Stone's drosophila presentation and Lacey Sanderson's Tripal/Drupal presentation were the most interesting.
  • Tripal Project Update
  • Evo Hackathon jbrowse satellite meeting.
  • All the sessions were very interesting and useful. I enjoyed the intro to GMOD session tremendously, as it was a very nice setup for the rest of the meeting. I found the 'showcasing' of different GMOD modules very useful--since we are at the stage of making decisions as to which components to start our project with, that was very useful. The most useful, however, were many of the conversations and discussions I had throughout the meeting, as well as the satellite session on JBrowse.
  • The component presentations (JBrowse, Tripal, Galaxy, etc).
  • Honestly, all of the presentations were useful. While coming at things from an IT perspective, hearing the real life practical applications of the software was important.
  • JBrowse, State of GMOD, Tripal, Flybase.
  • Besides the updates, Eric Stone's presentation was fascinating. I enjoyed the discussions in the break out groups on Monday. Great interaction among attendees and with speakers.
  • I enjoyed and learned a lot from the the Intermine, modware and Tripal presentations.
  • Dave E from flybase, Eric Stone, Scott Cain, Mitch JBrowse, Intermine, ..., the list goes on and on very very good.
  • Satellite Meetings because is allows a more straight line of communication instead of a presentation. It is more dynamic and it tends to address the questions on less casual manner.
  • Mimosa & JBrowse presentations
  • All were interesting. The most useful for my work directly were as follows. Introductions The State of GMOD GMOD Help Desk Update Mashing up InterMine: An introduction to the new InterMine webservice features JBrowse Project Update Tripal Project Update Galaxy for high-throughput sequence data analysis Implementation of RNA-Seq data in Chado at FlyBase
  • I'm new to GMOD, so they were all useful! For me, GBrowse and Chado are the core applications that I'm seeking to implement, so the presentations by Scott Cain and Dave Emmert were especially interesting to me


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

  • Scott could stand to be slightly more ... not cutting people off, but maybe keeping people moving at some slow points.
  • Figure out agenda earlier
  • Maybe more tutorials of the software being presented.
  • I would recommend having a more diverse organizing committee, one with a collectively broad view, and to include more unconference elements.
  • Not at this time: I think it strikes a good balance.
  • The lightning talks probably ought to be truly lightning (short) and maybe limited to a time frame.
  • Depending on the skill level/interests of attendees, it might be useful to present a list of satellite meetings before the meeting. People can then vote even before they come.
  • No, they seem to be well run. Perhaps getting people to think about hackathon-ish ideas before the meeting would be useful.
  • I think GMOD needs to grow it's prestige and team with a Journal to publish papers on bioinformatics databases and system integration. As we enter the world of data driven science, tools and complex algorithms are no longer sufficient... we need better data models and better ways to integrate biology. Funding and advancement comes from sharing... and management looks at sharing/support of software as less important than sharing scientific results. GMOD as a community is one of the few organisations who can change this.
  • Kidnap Dave.
  • Great organization, not really (I'm not sure if this is a positive or a negative comment.)
  • This meeting was a little disorganized. I would like to have the schedule finalized more than 1 week before the conference. I really liked the introduction to GMOD on Friday night. I think a little bit more about how the various programs interact and compare/contrast between those that do similar things would be Really useful!
  • More examples, especially for plant, will be better.
  • More veggies for snacks!