3149
Plant Science at the JGI and KBase

The Department of Energy currently funds both a large scale user facility for plant genomics at the DOE Joint Genome Institute and a large scale computational resource for comparative functional genomics and systems biology of microbes, plants and their communities called the DOE Systems Biology Knowledgebase (KBase). The core mission of both of these endeavors is to help scientists carry out experiments and analyses in areas such as improving biofuel development, understanding plant model systems, advancing plant comparative science and investigating global carbon cycling. In this workshop, we will present current and ongoing developments from both the Plant Program at JGI and KBase toward integrative biology. We will also hear from researchers who are applying genomic sequence information from JGI to elucidate functions of plant systems and from users who are working to apply KBase computational infrastructure to plant biological inquiries. We will describe how to apply for a project with the JGI Community Science Program and how you can use the KBase system to accelerate your plant genomics research.
Date: Tuesday, January 12, 2016
Time: 4:00 PM-6:10 PM
Room: San Diego
Organizers:
Gerald A. Tuskan , Doreen Ware , Jeremy Schmutz and Dave Weston
4:00 PM
Joint Genome Institute Plant Science Program
Jeremy Schmutz, DOE Joint Genome Institute; Kerrie W. Barry, DOE Joint Genome Institute; David M. Goodstein, DOE Joint Genome Institute; Jane Grimwood, HudsonAlpha Institute for Biotechnology; Uffe Hellsten, DOE Joint Genome Institute; Jerry Jenkins, DOE Joint Genome Institute; John P. Vogel, Department of Energy Joint Genome Institute; Gerald A. Tuskan, Oak Ridge National Laboratory; Daniel S. Rokhsar, DOE Joint Genome Institute

4:20 PM
4:35 PM
JGI Plant Gene Atlas: Adding Experimentally Derived Functional Annotations to JGI Plants
Avinash Sreedasyam, HudsonAlpha Institute for Biotechnology; Christopher Plott, HudsonAlpha Institute for Biotechnology; Morgan Qualls, HudsonAlpha Institute for Biotechnology; Jerry Jenkins, HudsonAlpha Institute for Biotechnology; Jane Grimwood, HudsonAlpha Institute for Biotechnology; Joseph W. Carlson, DOE Joint Genome Institute; David M. Goodstein, DOE Joint Genome Institute; Thomas Juenger, University of Texas; Yuhong Tang, The Samuel Roberts Noble Foundation; Gerald A. Tuskan, Oak Ridge National Laboratory; Thomas P. Brutnell, Enterprise Institute for Renewable Fuels Donald Danforth Plant Science Center; Sabeeha S. Merchant, University of California; Stefan A. Rensing, Faculty of Biology, University of Marburg; John Mullet, Texas A&M University; Todd C. Mockler, Donald Danforth Plant Science Center; Gary Stacey, University of Missouri; Jeremy Schmutz, HudsonAlpha Institute for Biotechnology

4:55 PM
Progress Towards an Engineering Quality Sorghum Reference Genome Sequence
John Mullet, Texas A&M University; Jeremy Schmutz, HudsonAlpha Institute for Biotechnology; Jerry Jenkins, HudsonAlpha Institute for Biotechnology; David Sims, HudsonAlpha Institute for Biotechnology; Jane Grimwood, HudsonAlpha Institute for Biotechnology; Brian McKinley, Texas A&M University; Daryl Morishige, Texas A&M University; Brock D. Weers, Texas A&M University; Ashley Mattison, Texas A&M University; Ryan McCormick, Texas A&M University; Sandra Truong, Texas A&M University

5:15 PM
The Pan-Genome of Brachypodium distachyon, Capturing the Full Genetic Complement of a Plant Species
John P. Vogel, DOE Joint Genome Institute; Sean Gordon, DOE Joint Genome Institute; Bruno Contreras-Moreira, Fundación ARAID; David L. Des Marais, Harvard University; Diane Burgess, University of California; Wendy Schackwitz, DOE Joint Genome Institute; Ludmila Tyler, Biochemistry and Molecular Biology Department; Joel Martin, DOE Joint Genome Institute; Daniel Woods, University of Wisconsin-Madison; Richard Amasino, University of Wisconsin-Madison; Anna Lipzen, DOE Joint Genome Institute; Shengqiang Shu, DOE Joint Genome Institute; Jeremy L. Phillips, DOE Joint Genome Institute; Kerrie W. Barry, DOE Joint Genome Institute; Ana Caicedo, Biology Department, University of Massachusetts; Luis Mur, Aberystwyth University; Michael R Freeling, University of California; Pilar Catalan, Department of Agriculture (Botany), High Polytechnic School of Huesca, University of Zaragoza

5:45 PM
When Biologists and Modelers Meet in KBase: Case Example of Modeling Plant-Microbe Metabolic Interactions
Dave Weston, Oak Ridge National Laboratory; Samuel M. D. Seaver, Argonne National Laboratory

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