GMOD
PAG 2011
GMOD had a strong presence at the Plant and Animal Genome Conference (PAG XIX) again this year. For the first time, there was an all-day dedicated GMOD Workshop at PAG. The workshop included sessions on MAKER, Galaxy, Tripal, JBrowse and GBrowse_syn. The workshop was in addition to the hands-on GBrowse tutorial that is offered every year. As in past years (see PAG 2010 and PAG 2009), there were also many workshops, computer demos, and posters, either about GMOD and GMOD Components, or using GMOD components.
Contents
About GMOD Components
This list will become more populated as the program finalizes.
Projects Using GMOD Components
| Day | Track | Time | Title & Presenter | Components |
|---|---|---|---|---|
| Saturday Jan 15 |
Computer Demos | 2:30-2:50 | Using SGN Resources After The Tomato Genome Sequencing, Aureliano Bombarely | Chado, Bio%253A%253AChado%253A%253ASchema, GBrowse, BLAST_Graphic_Viewer |
| 2:50-3:10 | GDR (Genome Database For Rosaceae): Building Resources For Translational Research In Rosaceae, Sook Jung | Chado, CMap, GBrowse, Tripal | ||
| Workshops | 4:40-5:00 | Development Of cBARBEL, A Catfish Genome Database, Jianguo Lu | GBrowse | |
| 5:00-5:20 | Use Of A Minimum Tile Path For Discovery Of Genes Altering Plant Development By Plant Transformations Encompassing The Entire Soybean Genome, David A Lightfoot | GBrowse | ||
| Sunday Jan 16 |
Workshops | Exploiting Sorghum Resources For The Molecular Mapping Of Sugarcane, Yogesh Parmessur | GBrowse | |
| 2:30-2:50 | GNPAnnot Community Annotation System Applied To Sugarcane BAC Clone Sequences, Valentin Guignon | Apollo, Chado, GBrowse | ||
| 3:00-3:20 | Bio-informatic resources for genomic and genetic information system in grapevine, Anne-Francoise Adam-Blondon | Apollo, BioMart, Chado, CMap, Galaxy, GBrowse | ||
| 3:45-4:00 | Towards Developing A Comprehensive Genomics, Genetics And Breeding Database For Cacao Improvement, Ping Zheng | Chado, CMap, GBrowse, Tripal | ||
| Computer Demos | 3:50-4:10 | Accessing Information In Plant Metabolic Pathway Databases At The Plant Metabolic Network, Gramene, And The SOL Genomics Network, Kate Dreher | Pathway Tools | |
| Monday Jan 17 |
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| Tuesday Jan 18 |
Workshops | 1:40-2:05 | The Genetic Map And Genome Sequencing Of Lettuce, Richard Michelmore | GBrowse |
| Wednesday Jan 19 |
Posters
| Track | Time | Title & Author | Components |
|---|---|---|---|
| EVEN Numbered Poster Session Monday Jan 17 |
10:00-11:30 | P020 Applying Second Generation Sequencing Technology For The Analysis Of Isolated Wheat Chromosomes, Paul J Berkman, et al. | GBrowse |
| P038 The Amborella Genome Project: Generating A Reference Sequence For Angiosperm Evolutionary Analysis, Srikar Chamala, et al. | GBrowse | ||
| P188 Development Of A Galaxy Workflow For SNP Detection In Grapevine And Poplar Whole Genome Illumina Resequencing Data, Nathalie Choisne, et al. | Galaxy | ||
| P790 New Transcriptome Data And Tools At The Comparative Evolutionary Genomics Of Cotton Web Resource, Alan R. Gingle, et al. | GBrowse | ||
| P796: MOCCAdb - An Integrative Database For Functional, Comparative And Diversity Studies In The Rubiaceae Family, Christine Tranchant-Dubreuil | CMap | ||
| P798 CottonDB: An Integrated Repository Resource For Cotton, Jing Yu, et al. | CMap, GBrowse | ||
| P800 Genome Annotation And Report System: An Integrated System For Structural And Functional Genome Annotation, Joelle Amselem, et al. | Apollo, Chado, GBrowse, GBrowse_syn, BioMart | ||
| P814 Informatics For Turbo-Charged Comparative Biology: Highlights From The GMOD Tools For Evolutionary Biology Hackathon, Robert Buels, et al. | Chado, Galaxy, GBrowse_syn, JBrowse (GMOD Evo Hackathon) | ||
| P818 A Complete Community Annotation System Using GMOD Tools, Scott Cain, et al. | Apollo, BioMart, Chado, GBrowse, MAKER, Tripal | ||
| P820 Triannot: A User Friendly Web Interface For Structural And Functional Automatic Annotation Of Plant Genomes, Philippe Leroy | GBrowse | ||
| P828 GBrowse 2.2: Fast, Friendly And Sociable (pdf), Anthony deCatanzaro, et al. | GBrowse | ||
| P888 GDR (Genome Database For Rosaceae): Building Resources For Translational Research In Rosaceae, Sook Jung, et al. | chado, CMap, GBrowse, Tripal | ||
| Track | Time | Title & Author | Components |
| ODD Numbered Poster Session Monday Jan 17 |
3:00-4:30 | P513 Gene Evolution In Metabolic Pathways Of The Cattle Genome, Woonsu Kim, et al. | BioMart |
| P805 Gnpis, A Portal And Information System To Bridge Genetics And Genomics Plant And Fungi Data, Delphine P Steinbach, et al. | BioMart, Galaxy | ||
| P891 Accessing Information In Plant Metabolic Pathway Databases At The Plant Metabolic Network, Gramene, And The SOL Genomics Network, Kate Dreher, et al. | Pathway Tools | ||
Roadshow
As shown above, GMOD will have a large number of representatives at PAG XIX. Three of them, Dan Blankenberg of the Galaxy project, Mitch Skinner, lead JBrowse developer, and Scott Cain, GMOD Project Coordinator, are available to visit organizations in the San Diego area during the conference.
If you would like to arrange a visit with Dan, Mitch, and/or Scott to discuss Galaxy, JBrowse, or any other GMOD Components, please contact Dan, Mitch and Scott directly.
Flier
A flier highlighting some of the GMOD-related content at PAG XIX is available. Hard copies of this flier will be available at the conference. If you will be presenting at PAG, please feel free to print out several copies and make them available at your talk or poster.