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PAG 2011

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PAG 2011 Conference

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.

About GMOD Components

This list will become more populated as the program finalizes.

Day Track Time Title & Presenter Components
Saturday
Jan 15
Sunday
Jan 16
Computer & Training Workshop 8:00-9:00 Ensembl and Ensembl Genomes, Bert Overduin BioMart
1:30-3:40 The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse, Scott Cain. GBrowse
Computer Demon-
strations
4:30-4:50 How to Use MetaCyc and the Pathway Tools Software in Local Mode, Lukas Mueller Pathway Tools
Monday
Jan 17
Tuesday
Jan 18
Computer & Training Workshop 3:50-6:00 Using Gramene: A Genomics and Genetics Resource for Rice and other Grasses, Ken Youens-Clark CMap
Wednesday
Jan 19

Computer & Training Workshop
10:20-5:00

GMOD Workshop: Organize, Annotate, and Visualize Your Data, Scott Cain, Dave Clements, Pacific Salon 3
10:20-10:30 Introduction, Scott Cain
10:30-11:30 MAKER: An easy to use genome annotation pipeline, Carson Holt, Barry Moore, Robert Ross MAKER
11:30-12:30 Galaxy: Analyze, Visualize, Communicate, Dan Blankenberg Galaxy
1::30-2:30 JBrowse: A Next Generation Genome Browser, Mitch Skinner JBrowse
2:30-3:30 Tripal: A Construction Toolkit for Online Genomic Databases, Stephen Ficklin Tripal
3:45-4:00 GMODviews: a web-based knowledge-base and user-configurable interface for GMOD databases and tools, including Tripal, GBrowse, and Chado, Michael Caudy GMODviews
4:00-5:00 GBrowse_syn: The Generic Synteny Browser, Robert Buels GBrowse_syn

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::Chado::Schema, 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
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

GMOD San Diego 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.

See Also