NOTE: We are working on migrating this site away from MediaWiki, so editing pages will be disabled for now.
March 2011 GMOD Meeting
__NOTITLE__
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.
G M O D A M E R I C A S 2 0 1 1 |
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 |
Agenda
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: | ||
Chris Hemmerich | |||
Chris Hemmerich | |||
|
|||
|
Siddhartha Basu | PPT, Slideshare | |
|
Tom Walk | PPT | |
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 | :Image:GMODAmericas2011Flier.pdf}} |
Logistics
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.
Feedback
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.