March 2011 GMOD Meeting
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.
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.
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.
|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 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.
|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||PPT|
|10:50||GMOD Help Desk Update||Dave Clements||PPT|
|1:15||Drosophila Genetic Reference Panel (DGRP)||Eric Stone|
|2:00||GSA and GMOD||Elizabeth Ruedi||PPT|
|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||Slides|
|11:10||Galaxy for high-throughput sequence data analysis||Dave Clements|
|1:00||Implementation of RNA-Seq data in Chado at FlyBase||Dave Emmert||Slides|
|Siddhartha Basu||PPT, Slideshare|
Monday: Satellite Meetings
|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.
See the GMOD Americas 2011 page for information on lodging, transportation and meals.
Attendees were asked to provide feedback at the end of the meeting.
Q: Would you recommend GMOD meetings to others
- 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).
|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?
- 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!