March 2011 GMOD Meeting
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.
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.
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 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.
|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.
|9am-5pm|| GMOD Community Meeting|
Talks and discussions on GMOD Components, project direction and planning, best practices, recent developments, extensions, ...
|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.
|All Day||2011 GMOD Spring Training|
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.
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.
- Eric Stone, The Drosophila Genetic Reference Panel
- Scott Cain, GMOD Project Update, including lots of details about GBrowse2.2
- Dave Clements, Galaxy Update, and GMOD Help Desk update
- Dave Emmert, Implementation of RNA-Seq data in Chado at FlyBase
- Elizabeth Ruedi, Genetics Society of America (GSA)
- Alex Kalderimis, Mashing up InterMine: An introduction to the new InterMine webservice features. Access to data in the browser through cross-domain friendly webservices.
- Jonathan "Duke" Leto, Mimosa: Miniature Model Organism Sequence Aligner, is a pluggable web application for sequence alignment (i.e. BLAST) written in Perl 5 and building upon BioPerl, Bio::Chado::Schema, Moose and the Dancer web framework.
- Lacey Sanderson, Tripal project update
- Kashi Revanna, A Light-weight Genome Synteny Visualization Web Server for Customized Data Display
- Siddhartha Basu (lightning talk), Modware, a middleware for Chado database, its latest development using Schema and Moose.
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.
|7pm-9m||Introduction to GMOD||Scott Cain|
Saturday: Day 1
|9:35||Welcome to NESCent, & opportunities at the center||Todd Vision||slides|
|9:50||The State of GMOD||Scott Cain|
|10:50||GMOD Help Desk Update||Dave Clements|
|11:10||Implementation of RNA-Seq data in Chado at FlyBase||Dave Emmert|
|1:15||Drosophila Genetic Reference Panel (DGRP)||Eric Stone|
|2:00||GSA and GMOD||Elizabeth Ruedi|
|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.
|9:15||JBrowse Project Update||Mitch Skinner||Slides|
|10:00||Tripal Project Update||Lacey Sanderson|
|11:00||Galaxy for high-throughput sequence data analysis||Dave Clements|
|11:30||Lightning talks: ISGA, a synteny browser, Modware and more!|
|1:15||More lightning talks, or extended demos|
Monday: Satellite Meetings
Meeting participants will be listed here as the meeting gets closer.
Confirmed participants thus far:
|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|
|Christopher||Hemmerich||Center for Genomics and Bioinformatics|
|Alex||Kalderimis||University of Cambridge, FlyMine, InterMine|
|Jonathan||Leto||Sol Genomics Network - Boyce Thompson Institute|
|Zhanji||Liu||Delaware State University|
|Trevor||Newell||Delaware State University|
|Daniel||Quest||Oak Ridge National Lab (JGI)|
|Elizabeth||Ruedi||Genetics Society of America (GSA)|
|Victor||Ruotti||Morgridge Institute for Research|
|Lacey-anne||Sanderson||University of Saskatchewan|
|Sheena||Scroggins||Polytechnic of NYU|
|Olen||Sluder||Texas Biomedical Research Institute|
|Tomasz||Smolinski||Delaware State University|
|Eric||Stone||North Carolina State University|
|Yaqoob||Thurston||Delaware State University|
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.