March 2011 GMOD Meeting

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GMOD Americas 2011}}


The next GMOD community meeting will be held March 5-6 2011, at NESCent in Durham, North Carolina, as part of GMOD Americas 2011, which also includes Satellite Meetings, and a GMOD Course.

For the first time, this meeting will be preceded by a GMOD Overview session the night before. This session is 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 course is 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. See the September 2010 GMOD Meeting page for an idea of what happens at a GMOD meeting.

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 is now open. The registration fee for the March 2011 GMOD Meeting is

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

The Satellite Meetings are free and registration is not required. You are, however, encouraged to sign up for a satellite in advance to show that there is interest.

The deadline to apply for the 2011 GMOD Spring Training has passed, but you can still get on waiting list.

GMOD Americas Events

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

Date Time Event
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.
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.

March 6
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.

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:

The course is currently full, but you can get on the waiting list.

Guest Speaker: Dr. Eric Stone

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

Our guest speaker is 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 will discus 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.

A detailed agenda will be posted shortly before the meeting.

Confirmed Speakers

Although a detailed agenda won't be available until the week before the meeting, we will list confirmed speakers and topics here as people commit.

Friday: Introduction to GMOD

This session the night before the meting will be an introduction to the GMOD project, community, and components. It is meant to give 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
10:35 Coffee
10:50 GMOD Help Desk Update Dave Clements
11:10 Implementation of RNA-Seq data in Chado at FlyBase Dave Emmert
11:55 Lunch
1:15 Drosophila Genetic Reference Panel (DGRP) Eric Stone
2:00 GSA and GMOD Elizabeth Ruedi
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
10:45 Break
11:00 Galaxy for high-throughput sequence data analysis Dave Clements
11:30 Lightning talks: ISGA, a synteny browser, Modware and more!
12:00 Lunch
1:15 More lightning talks, or extended demos

Monday: Satellite Meetings

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


Meeting participants will be listed here as the meeting gets closer.

Confirmed participants thus far:

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
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 :Image:GMODAmericas2011Flier.pdf}}


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

The meeting will be held in the A103 conference room of the Erwin Mill Building. A103 is on the ground floor of Erwin Mill, directly below NESCent. The Introduction to GMOD session on Friday evening will be help in NESCent's seminar room. Both events will have clear signs directing you to the appropriate room.


We will solicit feedback from meeting participants at the end of the meeting, and post it here once we have it.

Feedback on previous meetings (September 2010, January 2010, August 2009, January 2009, and 2008 and before) has been very positive.

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