Difference between revisions of "January 2010 GMOD Meeting"
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Revision as of 21:32, 21 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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This GMOD community meeting will be 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.
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. |
Agenda
Guest Speaker: Dr. Maryann Martone
Our special guest speaker was Dr. Maryann Martone, who discussed her work using ontologies in the field of 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 | |
11:00 | Report from the Help Desk | Dave Clements | PPT, PDF |
11:30 | Brief status updates: Satellite Meetings | ||
Josh Goodman | GMOD RPC API | ||
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 | |
2:15 | StrategiesWDK: intro to a powerful MOD-compatible search UI | Steve Fischer | StrategiesWDK, 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 Schema, 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 | PPT, PDF |
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 | PPT, PDF |
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 | ||
Mitch Skinner | |||
|
Ben Hitz | ||
|
Dawei Lin | ||
Stephen Ficklin | |||
|
Keiran Raine | PPT, PDF | |
Josh Goodman | |||
|
Maxim Troukhan | ||
Richard Smith | |||
|
Jonathan Crabtree | ||
|
Ram Podicheti | ||
5:30 | Finish |
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 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.)
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
Please provide feedback on this meeting.
Feedback on previous meetings has been very helpful to the organizers: