GMOD
January 2010 GMOD Meeting
| January
2010 GMOD Meeting January 14-15, 2010 San Diego, California, USA  |
|
This GMOD community meeting was held January 14-15, 2010, in San Diego, immediately following Plant and Animal Genome XVIII (PAG 2010). This meeting was full. Thanks to the generous support of USDA-ARS and NIH, registration for this meeting was free. Special thanks to Scott Markel and Accelrys for providing meeting equipment for us to use.
Contents
- 1 Agenda
- 2 Satellite Meetings
- 3 Meeting Participants
- 4 Agenda Proposals
- 5 Venue and Lodging
- 6 Feedback
- 7 Previous and Next Meetings
Agenda
Guest Speaker: Dr. Maryann Martone
The Neuroscience Information Framework: Establishing a practical semantic framework for neuroscience (PPT, PDF, ZIP)
Our guest speaker was Dr. Maryann Martone, who discussed her work using ontologies in neuroscience. Her research demonstrated the power of ontologies to bring together large volumes of disparate data into a unified whole using the semantic relationships that ontologies enable. Maryann is a Professor at UC San Diego, where she is the PI for the Neuroscience Information Framework (NIF), a web portal, providing simultaneous, deep web searches across multiple databases, web pages and literature. She is also Co-Director of the National Center for Microscopy and Imaging Research (NCMIR), where her research focuses on ontologies in image analysis and data mining tools.
Thursday, January 14
| Time | Topic | Presenter(s) | Links | |—-|—-|—-|—-| | 10:00 | Introductions and the State of GMOD | Scott Cain | PDF | | 11:00 | Report from the Help Desk | Dave Clements | PPT, PDF | | 11:30 | Brief status updates: Satellite Meetings | | | | | GMOD REST Hackathon | Josh Goodman | GMOD RPC API | | | BioPerl | Jason Stajich, Chris Fields | | | 12:30 | Lunch (catered on site) | | | | 1:30 | GMOD tools in the frame of GnpAnnot projects | Michael Alaux and Joelle Amselem | PDF | | 2:15 | StrategiesWDK: intro to a powerful MOD-compatible search UI | Steve Fischer | PPT, PDF | | 2:45 | Chado on Rails (Ruby on Rails and Chado) | Justin Reese, Chris Childers | Slides on Google Docs, PPT, PDF | | 3:15 | Coffee Break | | | | 3:30 | Using and developing Bio%253A%253AChado%253A%253ASchema, integrating it with other DBIx::Class-based code | Robert Buels | HTML | | 4:00 | Using Drupal and Flex to Create User-Configurable Interfaces for GMOD Databases for Use in Transcriptional Genomics Research | Michael Caudy | | | 4:30 | Discussion toward standard website platforms for MOD sites | | | | 5:00 | Dinner (on your own) | | |
Friday, January 15
| Time | Topic | Presenter(s) | Links | |—-|—-|—-|—-| | 9:00 | Textpresso | Nathan Liles | PPT, PDF | | 9:30 | TableEdit | Daniel Renfro, Jim Hu | PPT, PDF | | 10:00 | Adventures in NOSQL | Brian O’Connor, SeqWare | ODP, PDF | | 10:30 | Coffee break | | | | 10:45 | The Neuroscience Information Framework: Establishing a practical semantic framework for neuroscience | Maryann Martone | PPT, PDF, ZIP | | 11:30 | NCBO Tools and Web Services | Trish Whetzel | | | 12:00 | Lunch | | | | 1:15 | Providing a biologist-centered interface for running and customizing Ergatis pipelines | Chris Hemmerich | PPT, PDF | | 1:45 | Open Mic/Show and Tell | | | | | JBrowse | Mitch Skinner | PDF | | | Openings at SGD | Ben Hitz | | | | RediscoveryDB: Connecting High-Throughput Data with Testable Hypotheses | Dawei Lin | PDF | | | PhaseolusGenes : A Genomics Information Management and Marker Discovery Toolkit For A Non-Model Organism | Dawei Lin | PDF | | | Tripal | Stephen Ficklin | (PAG 2010 Talk) | | | Use of GBrowse 1.999 in the Cancer Genome Project | Keiran Raine | PPT, PDF | | | TopoView GBrowse glyph at FlyBase | Josh Goodman | PDF | | | Ceres Genome Browser | Maxim Troukhan | | | | InterMine | Richard Smith | HTML, PDF, | | | A Couple of UI Prototypes | Jonathan Crabtree | OpenOffice, PDF | | | WebGBrowse | Ram Podicheti | | | 5:30 | Finish | | |
Satellite Meetings
This year (for the first time I believe) there were satellite meetings in addition to the main meeting. Satellite meetings were about a particular topic or work area of interest that people wanted to spend more time on then they could during the main meeting.
| Topic | Organizer(s) | Comments |
|---|---|---|
| GMOD REST Hackathon | Josh Goodman (email) | I'd like to do a small GMOD REST API hackathon with a goal of
producing a working prototype at the end. Ideally I'd like to do a solid
day of coding activities but if you can only come for part of thetime
that is fine too.
I've posted a rough schedule and other information on the GMOD REST Hackathon page. |
| BioPerl | Jason Stajich, Chris Fields | This will be a meeting (possibly followed by a hackathon) that will
address BioPerl's current issues, future directions, etc. It is
anticipated that there will be overlap with other groups and satellite
meetings.
Sign up for the meeting and detail specific topics on the main BioPerl website. |
| Tripal Working Group | Stephen Ficklin | A discussion of Tripal with an
emphasis on future development plans. Anyone using Tripal, planning on
or interested in it, or with an interest in using Drupal as a web front
end to Chado is
encouraged to attend.
If you are interested, please add your name to the Tripal Working Group page. You may also want to subscribe to the Tripal mailing list. |
| Chado Natural Diversity Module Working Group | Dave Clements | A discussion of the Chado Natural Diversity Module, currently under development. |
Meeting Participants
| First Name(s) | Last Name | Affiliation | URL | |—-|—-|—-|—-| | Michael | Alaux | INRA, France | http://urgi.versailles.inra.fr/ | | Joelle | Amselem | INRA-URGI | http://urgi.versailles.inra.fr/ | | David | Arcoleo | Institute for Genomic Biology, University of Illinois, Urbana-Champaign | http://beespace.uiuc.edu | | Yuri | Bendana | USC BISC-MCB | | | Aaron | Buechlein | The Center for Genomics and Bioinformatics | | | Robert | Buels | SGN | http://solgenomics.net | | Scott | Cain | GMOD / OICR | http://gmod.org / http://www.oicr.on.ca/ | | Michael | Caudy | Reactome | http://www.reactome.org | | Chris | Childers | Bovine Genome Database; BeeBase; NasoniaBase; Hymenoptera Genome Database | http://bovinegenome.org; http://beebase.org; http://nasoniabase.org; http://hymenopteragenome.org | | Dave | Clements | GMOD / NESCent | http://gmod.org / http://nescent.org | | Jonathan | Crabtree | Institute for Genome Sciences / University of Maryland Baltimore | | | Stephen | Ficklin | Clemson University Genomics Institute | http://www.genome.clemson.edu/ | | Christopher | Fields | BioPerl, Institute for Genomic Biology | http://bioperl.org http://beespace.igb.uiuc.edu | | steve | fischer | EuPathDB | http://EuPathDB.org | | Eric | Ganko | Syngenta | | | Aureliano Bombarely | Gomez | Boyce Thompson Institute for Plant Research | http://solgenomics.net/ | | Josh | Goodman | FlyBase | http://flybase.org/ | | Chris | Hemmerich | Center for Genomics and Bioinformatics | http://cgb.indiana.edu/ | | LE, Quang | Hien | Vilmorin & Cie | http://www.vilmorin.info | | Ben | Hitz | SGD | http://www.yeastgenome.org/ | | Zhiliang | Hu | Iowa State University | http://www.animalgenome.org | | Jim | Hu | EcoliWiki | http://ecoliwiki.net | | Juan | Jovel | Scripps | | | John | Lee | USDA-ARS-WRRC-GGD | | | Nathan | Liles | Textpresso / GBrowse / EcoliWiki | http://textpresso.org | | Dawei | Lin | UC Davis | http://bioinformatics.ucdavis.edu/ | | Maryann | Martone | UC San Diego | Neuroscience Information Framework (NIF), National Center for Microscopy and Imaging Research (NCMIR) | | Sheldon | McKay | CSHL/iPlant | http://mckay.cshl.edu, http://iptol.iplantcollaborative.org | | Rex | Nelson | SoyBase | http://soybase.org | | Brian | O’Connor | GMODWeb | | | Youlian | Pan | National Research Council Canada, Ottawa / Arabidopsis / Brassica | http://www.nrc-cnrc.gc.ca/iit-iti/index.html | | Ram | Podicheti | Center for Genomics and Bioinformatics | http://www.cgb.indiana.edu/ | | Keiran | Raine | Cancer Genome Project (Wellcome Trust) - Human, Mouse | http://www.sanger.ac.uk/research/projects/cancergenome.html | | Justin | Reese | BeeBase/Bovine Genome Database/Hymenoptera Genome Database | http://bovinegenome.org; http://beebase.org; http://nasoniabase.org; http://hymenopteragenome.org | | Daniel | Renfro | EcoliWiki | http://ecoliwiki.net | | Lacey-Anne | Sanderson | Dept Plant Sciences, University of Saskachewan | | | Carl | Schmidt | University of Delaware / Gallus | | | Mitchell | Skinner | UC Berkeley | http://jbrowse.org | | Richard | Smith | University of Cambridge | http://www.intermine.org | | Jason | Stajich | BioPerl, FungalGenomes, University of California, Riverside | http://fungalgenomes.org/ | | Meg | Staton | Clemson University Genomics Institute | Tripal http://www.fagaceae.org http://www.rosaceae.org | | Jaideep | Sundaram | Computational Genomics Laboratory Georgetown University | | | Alexander | Tchourbanov | New Mexico State University, Biology Department | http://www.wyomingbioinformatics.org/~achurban/ | | Maxim | Troukhan | Ceres, Inc. | | | Trish | Whetzel | NCBO | | | Eric Kenneth | Wafula | Depamphilis Lab, Penn State university | http://depcla4.bio.psu.edu/ |
Agenda Proposals
If you have something you want to be on the agenda at this meeting please add it below.
- Using the 2009 GMOD Community Survey results for guidance – Dave Clements
- 2010 GMOD Summer Schools – Dave Clements
- GMOD tools in the frame of GnpAnnot projects (– Michael Alaux – Joelle Amselem, on the 14th)
- Using and developing Bio%253A%253AChado%253A%253ASchema, integrating it with other DBIx::Class-based code – Robert Buels
- Discussion toward standard website platforms for MOD sites – Robert Buels
- StrategiesWDK: intro to a powerful MOD-compatible search UI – Steve Fischer
- Give Textpresso meeting talk, Nathan Liles
- TableEdit, Daniel Renfro, Jim Hu, TableEdit on MediaWiki
- Providing a biologist-centered interface for running and customizing Ergatis pipelines – Chris Hemmerich
- Using Drupal and Flex to Create User-Configurable Interfaces for GMOD Databases for Use in Transcriptional Genomics Research – Michael Caudy
- Discussion/BoF for Hadoop & HBase. Our lab is starting to store next gen sequence data in HBase and I would be interested in talking with others interested building and deploying large genome database using these technologies. – Brian O’Connor
- Your suggestion here. (Login to edit this section.)
Venue and Lodging
The meeting was held at the Best Western Seven Seas, which is adjacent to the Town and Country Resort, where PAG is being held.
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% |
The maybe response was:
very technical so only to the right audience
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? | 5% | 0% | 19% | 38% | 38% |
| Was the meeting well run and organized? | 5% | 0% | 0% | 47% | 47% |
The “1” rating for both these questions came from the same person. However, that person was absolutely positive on all other questions. So, it’s possible they didn’t pay attention to if 1 was good or if 5 was good.
Q: Was the meeting what you expected?
| No. | Yes. | Other |
|---|---|---|
| 5% | 90% | 5% |
Longer responses:
- No, but that was a good thing. Informal atmosphere was great, felt much more comfortable asking questions. – the “no” response
- would have liked a little more discussion of what is new in gbrowse 2.0 – the “other” response
- Yes, I expected a lot of technical discussion about projects, and I had a number of ideas for improvement of our system.
- Yes, and it beat my expectations. I was expecting to hear about Gbrowse and Jbrowse but I also learned about Chado, data integration, NoSQL and ontologies.
- More than I expected.
Q: Which presentations and sessions at this meeting were the most useful or interesting?
- Update/overview of all GMOD projects (helps for Scott to run through all of them)
- StrategiesWDK was great but it was unclear how to integrate this in generic format to other projects.
- Introductions and the State of GMOD
- StrategiesWDK: intro to a powerful MOD-compatible search UI Steve Fischer StrategiesWDK, Using Drupal and Flex to Create User-Configurable Interfaces for GMOD Databases for Use in Transcriptional Genomics Research
- StrategiesWDK - saw this a something that could be used in our system, TableEdit - Nice to see something of a completely generic nature which simplifies something we all hate, NCBO - Did not know about this, we have a tissue ontology system which can be added, Ergatis - Appears to be an excellent system, may be able to implement internally with some extensions… future contribution?
- REST Hackathon, Strategies SDK, Open Mic session, Chado on Rails, * JBrowse, NoSQL
- StrategiesWDK: intro to a powerful MOD-compatible search UI, Chado on Rails, Using and developing Bio%253A%253AChado%253A%253ASchema, integrating it with other DBIx::Class-based code, The Neuroscience Information Framework: Establishing a practical semantic framework for neuroscience, JBrowse
- StrategiesWDK: intro to a powerful MOD-compatible search UI
- Rob Buell’s Bio%253A%253AChado%253A%253ASchema
- The NIF keynote presentation, Bio%253A%253AChado%253A%253ASchema, StrategiesWDK, Status updates/help desk”
- gnpAnnot, Ergatis pipeline, StrategiesWDK
- Steve Fischer’s query trees demo was intriuging - it’s a great way for user to dive into the data, TopoView GBrowse glyph at FlyBase - very cool, The Ergatis demo was interesting, but seems too complicated to use elsewhere.
- The data integration presentations (InterMine, Strategies) were very useful, since I hadn’t seen these before. The Drupal/Flex was also interesting and well as the Ergatis pipeline tool. The Chado related ones were good since I wasn’t that familiar with Chado. This has motivated me to install Chado/PostgreSQL and get to know them better and possibly use it for phenotype data. The NoSQL talk was good too because I haven’t heard much about distributed db. I liked The NIF talk since I haven’t had much exposure to ontologies. I also liked the final afternoon where people can go up and give demos.
- O’Conner (NOSQL), Caudy (Drupal), Martone (NIF), Skinner (JBrowse), in general talks that describe GMOD tools briefly, to orient us to what they do”
- Using and developing Bio%253A%253AChado%253A%253ASchema, GnpAnnot projects, Chado on Rails
- JBrowse, bioperl & DBIx, tripal, show and tell
- Representation of next generation sequences in GBrowse.
- The “current state of GMOD” presentations by Scott Cain, Dave Clements were very useful, as were the later updates on the release status of what you might call the core GMOD components (e.g., chado, GBrowse and also Mitchell’s talk on JBrowse.) I liked Michael Alaux’s presentation on the Chado Controller because it was an example of coming up with a general solution to a problem that other people might be able to use too. I thought Brian O’Connor’s “Adventures in NOSQL” was great because in 15 minutes he presented a bunch of useful information that it would take me hours to compile on my own. Dr. Martone’s invited talk was also excellent and very impressive and I thought the open mic session was also a great idea.
- TableEdit by Daniel Renfro, Jim Hu, Tripal by Stephen Ficklin
Q: Do you have suggestions for improving GMOD meetings in the future?
- Target a session on a particular topic – ie comparative genomics, or visualization, or data integration and queries. Focusing on how collaborative solutions can also be generated from the various projects so there is good level of communication.
- I like the free discussion style, but probably a little more time control would be better.
- Better WiFi or wired network connections
- Better time keeping. I think it is great to have a relaxed meeting but there should be some effort to keep talks close to the allocated time. I would prefer more time for the Open Mic, probably with a definite time limit on each. I was interested in the MODs using common web interface session which we never got to.
- Having a larger meeting may be helpful. Its great to see the broad range of topics. Many of them provide great ideas.
- The show-and-tell talks went a bit long. A bit more structure limiting time would be great.
- Perhaps a time for asking advice - I have this problem, or we use this setup. This happened on an ad hoc basis and was some of the more useful bits from the conference.
- I think some of the demos ran long, maybe have a 15 min time limit.
- humbly suggest that you consider enforcing time limits on talks, or with small grace periods. some seemed to go on too long. this would give latecomers on the agenda more time.
- Set up schedule in advance and uploading presentations a few days before the meeting for participants to have a chance to dig into what is to be presented.
- Limit show and tells to a reasonable amount of time (which will clearly be ignored, but the thought counts )
- Make it bigger by not limiting the number of participants.
- Definitely keep the open mic session but impose a strict (and short) time limit.
- If possible, to have the complete presentation agenda earlier.
Additional feedback, suggestions, criticism, and praise.
- Interoperability needs to be emphasized for some of the sets of disparate projects. Length, location, and timing was appropriate - tying the meeting to other conferences is a good thing. Consider genome informatics as well even if that is just an update meeting rather than a full blown 2-3 day affair.
- Thanks, well done
- I would most likely attend any meeting held in Europe if this was to go ahead as suggested.
- The Satellite meetings should happen again, adding a special interest day makes the travel more worthwhile.
- Wonderful job. Thanks for a great meeting.
- a little more enforcement of time limits would be a good idea!
- Thank you for a very well organized and informative meeting. It was a pleasure interacting over lunch and dinner as well with the other attendees. This allowed me to make a contact which will be helpful in completing a task in my job. Since I work alone on my project, it’s very helpful to interact with other bioinformaticians.
- Thanks for building the GMOD software, it makes life much easier.
- Good meeting, and it’s great that all the slides/presentations are going to be available online. Thanks!
Previous and Next Meetings
- August 2009 GMOD Meeting - Part of GMOD Europe 2009, Oxford, UK
- September 2010 GMOD Meeting - Part of GMOD Europe 2010, in Cambridge UK.