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Revision as of 19:37, 12 January 2010
January 2010 GMOD Meeting January 14-15, 2010 Following PAG 2010 San Diego, California, USA |
{{#icon: SanDiegoConvention.gif|San Diego Convention and Visitors Bureau | http://www.sandiego.org/nav/Visitors}} |
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The next GMOD community meeting will be held January 14-15, 2010, in San Diego, immediately following Plant and Animal Genome XVIII (PAG 2010). The meeting will be held at the Best Western Seven Seas (see Lodging below), which is adjacent to the Town and Country Resort, where PAG is being held.
The meeting is now full. However, you may get on the waiting list by filling out the registration form now.
Thanks to the generous support of USDA-ARS and NIH, registration for this meeting is free.
Guest Speaker: Dr. Maryann Martone
Professor, UC San Diego
Principal Investigator, Neuroscience Information Framework (NIF) | |
Our special guest speaker will be Dr. Maryann Martone, who will discuss her work on using ontologies in the field of neuroscience. Her research demonstrates 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. |
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 Schema, 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.)
Satellite Meetings
This year (for the first time I believe) there will be satellite meetings in addition to the main meeting. Satellite meetings are about a particular topic or work area of interest that people want to spend more time on then they can during the main meeting.
- Satellite meetings re self-organized. That is, if you want to get together with other people to discuss or work on a particular topic:
- Suggest a satellite meeting below, and on the appropriate GMOD Mailing Lists.
- Include your contact information and a suggested time and date.
- You may also want to create a wiki page for the satellite meeting.
- Satellite meetings take place outside the times of the main meeting.
- Satellite meetings have any particular space reserved for them. As the meetings crystallize, the GMOD Help Desk will be happy to help locate nearby facilities with free wifi.
Topic | Suggested Date | Organizer(s) | Comments |
---|---|---|---|
GMOD REST Hackathon | January 13, all day, starting at 9am | 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. If you want to attend please add your name to that page. |
BioPerl | January 13, all day, starting at 11am | 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 | January 13, 4-6pm | 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 | January 8, 5pm | Dave Clements | A discussion of the Chado Natural Diversity Module, currently under development.
If you are interested, please add your name to the working group page (once that page exists :-). |
Agenda
The final agenda will be posted shortly before the meeting. Please don't make changes to the agenda below without clearing it with Scott first (yes, I know it's a wiki ...)
Thursday, January 14
Time | Topic | Presenter(s) | Links |
---|---|---|---|
10:00* | Introductions and the State of GMOD | Scott Cain | |
11:00 | Report from the Help Desk | Dave Clements | |
11:30 | Brief status updates: Projects, satellite meetings, etc | misc | |
12:30 | Lunch (catered on site) | ||
1:30 | GMOD tools in the frame of GnpAnnot projects | Michael Alaux and Joelle Amselem | |
2:15 | StrategiesWDK: intro to a powerful MOD-compatible search UI | Steve Fischer | |
2:45 | Providing a biologist-centered interface for running and customizing Ergatis pipelines | Chris Hemmerich | |
3:15 | Coffee Break | ||
3:30 | Using and developing Bio::Chado::Schema, integrating it with other DBIx::Class-based code | Robert Buels | |
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) |
*Yes, we start at 10:00am on Thursday; the meeting room is unavailable before then.
Friday, January 15
Time | Topic | Presenter(s) | Links |
---|---|---|---|
9:00 | Textpresso | Nathan Liles | |
9:30 | TableEdit | Daniel Renfro, Jim Hu | |
10:00 | Something about key-value databases for scalable nextgen sequence databases | Brian O'Connor | |
10:30 | Coffee break | ||
10:45 | |||
11:15 | The Neuroscience Information Framework: Establishing a practical semantic framework for neuroscience | Maryann Martone | |
12:00 | Lunch | ||
1:15 | Open Mic/Show and Tell |
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 |
Muhammad | Ashraf | Agriculture & Agri-Food Canada | |
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 | |
david | elzinga | Undergrad working on EST annotation and Genome assembly at BYU(Utah) | |
Stephen | Ficklin | Clemson University Genomics Institute | http://www.genome.clemson.edu/ |
Christopher | Fields | Institute for Genomic Biology | |
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/ |
Gowthaman | Seattle Biomedical Research Institute | ||
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 | |
Anita | Lakatos | UCI | |
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 | |
RASHEED ABIODUN | ODUNTAN | NACGRAB | |
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 | |
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 | |
Jaideep | Sundaram | Computational Genomics Laboratory Georgetown University | |
Alexander | Tchourbanov | New Mexico State University, Biology Department | http://www.wyomingbioinformatics.org/~achurban/ |
Maxim | Troukhan | Ceres, Inc. | |
Eric Kenneth | Wafula | Depamphilis Lab, Penn State university | http://depcla4.bio.psu.edu/ |
Venue and Lodging
The meeting is being held at the Best Western Seven Seas, which is adjacent to the Town and Country Resort, where PAG is being held. Rooms are available to GMOD meeting participants at the special rate of $72/night plus tax. Rooms can be booked at this rate for the entire duration of PAG 2010 and this GMOD meeting. The hotel also offers a complimentary shuttle to and from the airport.
A room can be booked by calling +1 619 291 1300. Mention "GMOD" to get the special rate.
Feedback
Please provide feedback on this meeting.
Feedback on previous meetings has been very helpful to the organizers: