PAG 2010

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PAG 2010 Conference

GMOD once again had a strong presence at the Plant and Animal Genome Conference (PAG XVIII). There were many workshops, computer demos, and posters, either about GMOD and GMOD Components, or using GMOD components. This page lists the subset that mentioned GMOD or GMOD components in the abstract.

About GMOD Components

Carson Holt presenting the MAKER genome annotation pipeline at PAG.

There were a record nine talks and workshops either entirely or partially about GMOD Components. It was the first time Galaxy, MAKER, and JBrowse were presented at PAG. We also gave our first GMOD overview talk at PAG. There was a great dead of interest in GMOD and ll of the talks were well attended, with several of them being standing room only.

Day Track Time Title & Presenter Components
Jan 9
Computer & Training Workshop 1:30-2:30 Animal Genomics with Galaxy: Analyze, Publish, and Visualize, Dan Blankenberg Galaxy
3:50-6:00 MAKER: An easy to use genome annotation pipeline, Carson Holt MAKER
Jan 10
Computer & Training Workshop 8:15-9:15 Database Resources at the EBI: Ensembl And Ensembl Genomes - Access To Genome-Scale Data Across The Taxonomic Space, 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
Jan 11
Computer & Training Workshop 12:50-1:10 GMOD Project Update, Dave Clements, Scott Cain GMOD Components
1:10-1:30 Using the JBrowse Genome Browser with Large Amounts of Data, Mitch Skinner JBrowse
Jan 12
Computer & Training Workshop 3:50-6:00 Using Gramene: A Genomics and Genetics Resource for Rice and other Grasses, Ken Youens-Clark CMap
Jan 13
Computer & Training Workshop 10:20-12:30 Comparative Genomics with GBrowse_syn: Visualizing your comparative genomics data with the Generic Synteny Browser, Sheldon McKay GBrowse_syn
2:30-2:50 Tripal: a Construction Toolkit for Online Genomic Databases, Stephen Ficklin Tripal, Chado

Projects Using GMOD Components

Day Track Time Title & Author Components
Jan 9
Workshop 8:45-9:05 Full Genome Sequencing Of The Woodland Strawberry, Fragaria vesca, Vladimir Shulaev GBrowse
11:40-12:00 Development Of Tools For The Analysis And Visualisation Of Second Generation Sequencing Data For Brassica Species, Chris Duran CMap (CMap3D)
4:10-4:30 The Rice Annotation Project Database (RAP-DB): IRGSP/RAP Build 5 Annotation, Takeshi Itoh GBrowse_syn
Jan 10
Workshop 8:20-8:40 Epigenomic Analysis Of Populus trichocarpa Tissues From Differing Developmental Stages, Kelly J. Vining GBrowse
11:30-12:00 The Bovine Gene Atlas, Tad Sonstegard GBrowse
2:15-2:30 ConiferGDB: Current Status And Future Direction, Chun Liang CMap
3:50-6:00 TAIR Workshop, Eva Huala GBrowse, GBrowse_syn
Computer Demo 4:10-4:30 MaizeGDB: Tools and Resources, Carson Andorf CMap, GBrowse
4:30-4:50 How to Use MetaCyc, a Reference Database for Metabolism, and SolCyc, a Collection of Pathway Databases for the Solanaceae, on the Web and Using Pathway Tools, Lukas Mueller Pathway Tools
4:50-5:10 GDR in Drupal: Facilitating Community Building and Efficient Maintenance, Sook Jung Chado, Tripal
5:10-5:30 The Soybean Genome Database (SoyGD) Genomic Interactome Viewer, David Lightfoot GBrowse
5:30-5:50 PhaseolusGenes: A Genomics Information Management And Marker Discovery Toolkit For A Non-Model Organism, Dawei Lin CMap, GBrowse
5:50-6:10 Community Curation Software at the Sol Genomics Network (, Lukas Mueller Chado
Jan 11
Computer Demo 1:50-2:10 TreeGenes: A Forest Tree Genome Database, Jill Wegrzyn CMap
Jan 12
Workshop 11:55-12:10 Towards A Bioinformatics Platform For The Musa Research Community, Mathieu Rouard CMap, GBrowse


Titles of sessions that are about GMOD Components are shown in bold.

Track Time Title & Author Components
EVEN Numbered Poster Session
Jan 11
10:00-11:30 P150: The Use Of BES And Genome Sequence Derived Microsatellite Markers For QTL Discovery, Rabia Bashir, Samreen Kazi, David A Lightfoot GBrowse
P786: Bioinformatics Tools For Avian Genomics, Carl J Schmidt, Catalina O Tudor, li Jin, Keith S. Decker, Fiona McCarthy, Peter D'Eustachio, K-Vijay Shanker GBrowse
P830: The Hymenoptera Genome Database, Monica C. Munoz-Torres, Justin T. Reese, Christopher P. Childers, Anna K. Bennet, Jaideep P. Sundaram, Donald C Vile, Christine G. Elsik Apollo, Chado, GBrowse, GMODTools. XORT
P832: Design And Implementation Of The Cacao Genome Database, Ping Zheng, Sook Jung, Margaret Staton, Randall Svancera, Taein Lee, Stephen Ficklin, David N. Kuhn, Raymond J. Schnell, Juan Carlos Montamayor, Dorrie Main Chado, Tripal
P838: Bovine Genome Database Systems Infrastructure, Jaideep P. Sundaram, Christopher P. Childers, Justin T. Reese, Donald C. Vile, Christine G. Elsik Chado
P842: The Bovine Genome Database, Christopher P. Childers, Justin T. Reese, Jaideep P. Sundaram, Donald C. Vile, Darren E. Hagen, Anna K. Bennett, Christine G. Elsik Apollo, Chado, GBrowse, GMODTools, XORT
P858: GBrowse And Next Generation Sequencing Data, Scott Cain, Dave Clements, Lincoln Stein, the GMOD Consortium GBrowse
P914: The Rice Annotation Project Database (RAP-DB): IRGSP/RAP Build 5 Annotation, Takeshi Itoh, Tsuyoshi Tanaka, Hiroaki Sakai, Hisataka Numa, Naoki Amano, Hiroshi Ikawa, Takashi Matsumoto GBrowse_syn
Track Time Title & Author Components
ODD Numbered Poster Session
Jan 11
3:00-4:30 P016: Analysis Of Genomic Sequences From Lupinus luteus L., Héctor A Urbina Saavedra, Marcos R Olivos Trujillo, Cristell S Navarro Navarro, Lorena B Parra González, Gabriela A Aravena Abarzúa, Joshua A Udall, Shannon C Straub, Haroldo E Salvo Garrido, Iván J Maureira Butler GBrowse
P295: Wheat Genomic Data In GnpIS The URGI Information System Michael Alaux, Daphné Verdelet, Aminah-Olivia Keliet, Erik Kimmel, Baptiste Brault, Nacer Mohellibi, Benoit Hilselberger, Sophie Durand, Isabelle Luyten, Sébastien Reboux, Delphine Steinbach GBrowse
P513: Populus trichocarpa Epigenomics: Analysis Of The Developmental Poplar Methylome, Kelly J. Vining, Kyle R. Pomraning, Larry Wilhelm, Palitha D. Dharmawardhana, Henry D. Priest, Olga Shevchenko, Cathleen Ma, Ruoqing Zhu, Elizabeth Etherington, Todd Mockler, Michael Freitag, Steven Strauss GBrowse
P537: QTL, Hypothalamic-Transcriptome, And Candidate Gene Query Suggest Bovine Chromosome 2 Influences Heifer Pregnancy, Milton G Thomas, Sunday O Peters, Kadir Kazilkaya, Dorian J Garrick, Rohan L Fernando, James M Reecy, Z-L Hu, Faye D Schilkey, Robert L Weaber, Gail A Silver GBrowse
P599: Segmental Duplications In Pig Genome, Zhi-Qiang Du , Danielle M. Gorbach , Zhiliang Hu , Max F. Rothschild BioMart
P823: BRISKA: Brassica Seed Knowledge Base, Hugo Berube, Alain Tchagang, Yunli Wang, Ziying Liu, Sieu Phan, Fazel Famili, Youlian Pan Chado
P833: QTL Analysis, Visualization And The Link To Genomes At SGN Database, Isaak Y Tecle, Naama Menda, Robert Buels, Lukas Mueller GBrowse
P839: How To Use The New Functionalities At MaizeGDB: Now Sequence-Centric!, Lisa C. Harper, Mary L. Schaeffer, Taner Z. Sen, Carson M. Andorf, Ethalinda Cannon, Darwin A. Campbell, Lawrence Carolyn J. GBrowse
P851: SNPlotz: A Genome Plot Tool For SNP Association Studies, Zhi-Liang Hu, Rex Fernando, Dorian Garrick, James M. Reecy GBrowse
P859: Visualizing And Comparing Genomes, Ken Youens-Clark, Immanual V. Yap, Doreen Ware CMap
P861: Comparative Genomics Tools In GMOD, Dave Clements, Sheldon McKay, Ken Youens-Clark, Ben Faga, Scott Cain CMap, GBrowse_syn, Sybil, SynView, Apollo
P915: GDR In Drupal: Facilitating Community Building And Efficient Maintenance, Sook Jung, Randall Svancara, Meg Staton, Stephen Ficklin, Ping Zheng, Taein Lee, Dorrie Main GBrowse
P917: PhaseolusGenes: A Genomics Information Management And Marker Discovery Toolkit For A Non-Model Organism, Dawei Lin, Paul Gepts, Adam Schaal, Jose Boveda, JVG dos Santos, Joe Fass, Jim Kami, Nikhil Joshi, Monica Britton, Zhiwei Lu CMap, GBrowse
P919: Using The JBrowse Genome Browser With Large Amounts Of Data, Mitchell E Skinner, Andrew V Uzilov, Lincoln D Stein, Christopher J Mungall, Ian H Holmes JBrowse
P921: TreeGenes: A Forest Tree Genome Database, Jill L Wegrzyn, Ben Figueroa, Minyoung Choi, Elly Y Chen, David B Neale CMap


See Also