DOE Joint Genome Institute Strategic Planning for the Genomic Sciences Report from the May 30–31, 2012, Workshop Convened by U.S. Department of Energy Office of Science Office of Biological and Environmental Research Co-Chairs Jim Fredrickson Michael Laub Jan Leach Pacific Northwest National Laboratory Massachusetts Institute of Technology Colorado State University Breakout Group Chairs Richard Michelmore Kimmen Sjölander Tom Schmidt University of California, Davis University of California, Berkeley Michigan State University Organizer Daniel Drell [email protected], 301.903.4742 Web address for this document: genomicscience.energy.gov/userfacilities/jgi/futuredirections/ About the Cover Images on the cover represent a broad range of the complex scales encompassed by the science supported by the Office of Biological and Environmental Research (BER) within the U.S. Department of Energy’s (DOE) Office of Science. These scales range from genes at the subcellular level to genomes of microbes and their communities, to the genomics of plant-microbe interactions and plants that could be feedstocks for bioenergy, to the scale of ecosystem and landscape function. The under- lying DNA strand represents the DNA sequence data that provide the foundation for further systems-level experimentation. The images culminate in a wired cell that represents the predictive understanding of biological systems sought by BER programs. DNA sequence data generated by the DOE Joint Genome Institute user facility are having a major impact toward the achievement of this goal. Image credits: Microscopic images of organic matter decomposers (copyright Corbis), fungal hyphae on a root surface (copyright Corbis), and cross-section of a switchgrass stem (DOE BioEnergy Science Center and National Renewable Energy Laboratory). Grassland habitat (U.S. Department of Agriculture Natural Resources Conservation Service). Spruce-peatland ecosystem (Oak Ridge National Laboratory). Aerial view of Arctic landscape (Oak Ridge National Laboratory). Cover devel- oped at Oak Ridge National Laboratory. Suggested Citation U.S. DOE. 2012. DOE Joint Genome Institute Strategic Planning for the Genomic Sciences: Report from the May 30–31, 2012, Work- shop, DOE/SC-0152, U.S. Department of Energy Office of Science. DOE/SC-0152 DOE Joint Genome Institute Strategic Planning for the Genomic Sciences Report from the May 30–31, 2012, Workshop Published September 2012 Convened by U.S. Department of Energy Office of Science Office of Biological and Environmental Research DOE JGI Strategic Planning for the Genomic Sciences: Report from the May 30–31, 2012, Workshop ii U.S. Department of Energy Office of Science • Office of Biological and Environmental Research DOE JGI Strategic Planning for the Genomic Sciences: Report from the May 30–31, 2012, Workshop Contents Director’s Letter .................................................................................................................................................................................................................................... v Executive Summary .......................................................................................................................................................................................................................... vii Sidebar 1: Major Themes and Needs Emerging from the Workshop ................................................................................................................................... vii Introduction and Background ........................................................................................................................................................................................................1 Sidebar 2: Decreasing the Lag Time Between Sequencing and Annotation ........................................................................................................................2 Sidebar 3: DOE Biological and Environmental Research Program Perspective ....................................................................................................................3 Sidebar 4: DOE Genomic Science Systems Biology Program ...................................................................................................................................................5 Grand Challenges ................................................................................................................................................................................................................................9 Next-Generation Enabling Capabilities ...................................................................................................................................................................................13 Sidebar 5: Functional Annotation: A Prerequisite for Predictive Biology ...........................................................................................................................15 Sidebar 6: Automating Science in a Robotic Laboratory .......................................................................................................................................................19 Summary ..............................................................................................................................................................................................................................................21 Appendices ...........................................................................................................................................................................................................................................23 Appendix 1: Grand Challenges ..........................................................................................................................................................................................................23 Appendix 2: Department of Energy Assets ......................................................................................................................................................................................29 DOE Joint Genome Institute .....................................................................................................................................................................................................29 DOE Environmental Molecular Sciences Laboratory .............................................................................................................................................................30 DOE Systems Biology Knowledgebase ....................................................................................................................................................................................31 DOE Synchrotron and Neutron Beam Facilities for Biology ..................................................................................................................................................32 Appendix 3: Workshop Agenda, Charge Questions, Participants .................................................................................................................................................33 Appendix 4: Bibliography ..................................................................................................................................................................................................................37 Appendix 5: Glossary ..........................................................................................................................................................................................................................39 Acronyms and Abbreviations ................................................................................................................................................................................Inside back cover U.S. Department of Energy Office of Science • Office of Biological and Environmental Research iii DOE JGI Strategic Planning for the Genomic Sciences: Report from the May 30–31, 2012, Workshop iv U.S. Department of Energy Office of Science • Office of Biological and Environmental Research DOE JGI Strategic Planning for the Genomic Sciences: Report from the May 30–31, 2012, Workshop Department of Energy Washington, DC 20585 September 20, 2012 In October 2011, the U. S. Department of Energy (DOE) Joint Genome Institute (JGI) issued a draft “10-Year Strategic Vision: Forging the Future of the DOE JGI.” This document provided a high-level overview of DOE JGI and its plans to evolve as a next-generation genomic science user facility. The intent was to draft a vision for DOE JGI that goes beyond just sequence generation and seeks new technologies and/or capabilities to enhance the interpretation and use of genomic data. The draft document took advantage of a recent assessment (Grand Challenges for Biological and Environmental Research: A Long-Term Vision DOE/SC-0135) of the major long-term scientific challenges in energy and the environment that are the core mission areas of the DOE Office of Biological and Environmental Research (BER) and outlines how DOE JGI must evolve to help meet these research challenges. In May 2012, BER hosted a separate workshop on “DOE JGI Strategic Planning for the Genomic Sciences” to solicit additional community input towards articulating a high-level DOE Office of Science vision for DOE JGI’s role in advancing BER mission science. The intention was not to explore how DOE JGI could evolve to be a