Computational Sciences within NIGMS Protein Ontology Meeting, Georgetown, June 18, 2014 Veerasamy “Ravi” Ravichandran, Ph.D. Program Director Biomedical Technology, Bioinformatics and Computational Biology NIGMS/NIH

CASC-2014 National Institutes of Health 2 2 National Library of Medicine National Center for Advancing Translational Science National Institute of Nursing Research National Institute of Neurological Disorders and Stroke National Institute on Minority Health and Health Disparities Clinical Center Center for Scientific Review Center for Information Technology National Center for Complementary and Alternative Medicine National Institute on Drug Abuse National Institute of Environmental Health Sciences National Institute of General Medical Sciences National Institute of Diabetes and Digestive and Kidney Diseases National Institute on Deafness and Other Communication Disorders Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institute of Biomedical Imaging and Bioengineering National Institute of Mental Health National Institute of Dental and Craniofacial Research National Cancer Institute National Eye Institute National Heart, Lung, and Blood Institute National Human Genome Research Institute National Institute on Aging National Institute on Alcohol Abuse and Alcoholism National Institute of Allergy and Infectious Diseases National Institute of Arthritis and Musculoskeletal and Skin Diseases Office of the Director John E. Fogarty International Center for Advanced Study in the Health Sciences 27 Institutes and Centers

CASC-2014 NIGMS Organizational Chart 3 Office of Emergency Care Research Jeremy Brown, M.D. Director v v v v Biomedical Technology Branch v v Bioinformatics and Computational Biology Branch

CASC NIGMS Mission Promote fundamental research on living systems to lay the foundation for advances in disease diagnosis, treatment and prevention. Enable the development of the best trained, most innovative and productive biomedical workforce possible.

CASC-2014 NIGMS Budget Percentage Share by Mechanism FY 2013 Appropriation 5 5 RPGs: R00 R01 R15 R21 R37 P01 DP1 DP2 U01

CASC Targeted support for specific areas of research increased during the budget doubling Jim Deatherage, NIGMS

CASC-2014 Biomedical Technology, Bioinformatics and Computational Biology Division 7  Develop innovative tools and methods to understand biological systems, from molecular and subcellular to physiological and to population scales  Support multidisciplinary research and rapid translation of new technologies to biomedical researchers  Create training opportunities that are scientifically integrative and interdisciplinary

CASC-2014 BBCB’s Funding Mechanism 8 R01 (Research Projects Grants) R03 (Small Research Grants) R13 (Conference Grants) R15 (Academic Research Enhancing Awards, AREA) R21 (Exploratory/Developmental Award) R24 (Resource-Related Research Projects) R25 (Education Projects; courses, training, evaluation) R41/42 (Small Business Technology Transfer, STTR, grants) R43/44 (Small Business Innovation Research, SBIR, grants) P01 (Research Program Projects) P41 (Research Program Centers; e.g., BTRR) P50 (Research Program Centers; e.g., Systems Biology Centers) U01/U24/U27 (Cooperative agreements) T32 (Pre-doctoral Training; investigator-initiated) F31 (Individual pre-doctoral fellowship) F32 (Individual post-doctoral fellowship) F33 (senior scientists, change in the direction of research)

CASC-2014 Biomedical Technology, Bioinformatics and Computational Biology Research Enterprise 9 Biomedical Technology Research Resources Centers are unique and multidisciplinary in the development and rapid translation of new technologies that transform our approach in understanding biomedical problems. Instrumentation and Technologies for Biomedical Applications Technology-driven, investigator-initiated research in new or improved instruments, technologies, devices and methodologies that have broad application to biomedical research.

CASC Biomedical Technology, Bioinformatics and Computational Biology Research Enterprise Computational and Systems Biology New approaches, algorithms and methods for an integrative understanding of complex biological processes Mathematical and Statistical Modeling Promote research at the interface of the biological and mathematical sciences. MIDAS - Modeling of Infectious Disease Agent Study Collaborative research to model the dynamics of infectious diseases Data Sciences New shared computing algorithms and bioinformatics methods to manage, visualize and analyze complex scientific data, including standards and ontology

CASC Biomedical Technology Research Resources (P41) Multidisciplinary development, rapid application, and translation of new technologies that change our approach to biomedical problems. Technology R&D  Instruments, software, methods  Multidisciplinary  Science  Engineering  Medicine Driving Biomedical Projects  Intensive collaborations with biomedical laboratories  Translational  pushes limits of technology Collaboration and Service  biomedical research projects  access  technical assistance Training  peer training  use of center technology  workshops, courses, and symposia Dissemination  direct distribution  commercialization  workshops and symposia Technical innovations solve problems. Problems drive technologies.

CASC Resource for Analysis, Visualization, and Integration of Networks (RAVIN) P41 funding mechanism PI: Trey Ideker, UCSD Data-driven Science o Data-driven Ontology Network-extracted Ontology (NeXO)

CASC-2014 BBCB supported Ontology Related Programs 13 R01s: 1. Title: Collaborative Development of Biomedical Ontologies and Terminologies PI: Mark Musen, Stanford University 2. Title: PRO: A Protein Ontology in OBO Foundry for Integration of Biomedical Knowledge PI: Cathy Wu, University of Delaware Training grants (T32s): 1. Title: Biological and Medical Informatics (BMI) Ph.D. program (pre- doctoral) PI: Patricia Babbitt, UCSF 2. Title: Training Program in Bioinformatics PI: Brian Athey, University of Michigan

CASC-2014 BBCB Partnerships 14 Biomedical Information Science and Technology Initiative (BISTI) Promote the optimal use of computer science and technology to address problems in biology and medicine by fostering collaborations and interdisciplinary initiatives Big Data to Knowledge Initiative (BD2K) Develop new approaches, standards, methods, tools, software and competencies that will enhance the use of biomedical Big Data by supporting research, implementation and training in the data sciences Interagency Modeling and Analysis Group (IMAG) Provide an open forum for communication among government representatives for trans- agency activities that have a broad impact in science NSF/NIGMS Initiative to support research at the interface of biological and mathematical sciences NIH/DOE Partnership for stewardship of synchrotron beamlines for structural biology and other national laboratory BTRC activities

CASC Biomedical Information Science and Technology Initiative (BISTI) Consortium of representatives from each of the NIH institutes and centers Established in May 2000 to serve as the focus of biomedical computing issues at the NIH To make optimal use of computer science and technology to address problems in biology and medicine by fostering new basic understandings, collaborations, and transdisciplinary initiatives between the computational and biomedical sciences. (Susan Gregurick, Director, BBCB)

CASC New BISTI Funding Opportunities Early Stage Development of Technologies in Biomedical Computing, Informatics, and Big Data Science (R01) PA and (R43/R44) PA Major themes of research include: ⁻ collaborative environments and technologies ⁻ data integration ⁻ analysis and modeling methodologies; ⁻ novel computer science and statistical approaches. ⁻ This initiative aims to address biomedical research areas in biomedical computing, informatics, and big data science through the early stage development of new software, tools and related resources, as well as the fundamental research (e.g., methodologies and approaches) leading up to that development. Cross-disciplinary collaborations are strongly encouraged

CASC-2014 New BISTI Funding Opportunities 17 Extended Development, Hardening and Dissemination of Technologies in Biomedical Computing, Informatics and Big Data Science (R01) PA and (R41/R42) PA Major themes of research include: ⁻ collaborative environments and technologies ⁻ data integration ⁻ analysis and modeling methodologies; ⁻ novel computer science and statistical approaches. The proposed work should apply best practices and proven methods for software design, construction, and implementation to extend the applicability of existing technologies in biomedical computing, informatics and big data science to a broader biomedical research community Cross-disciplinary collaborations are strongly encouraged

CASC-2014 BD2K: Facilitating the broad use of data 18 Making Data Available o Recommending to change the policies, practices and culture of communities with regard to data Enabling Research Use of Clinical Data Making Data Usable 1. NIH Standards Information Resource To collect, organize and make available to the public trusted, systematically organized, and curated information about data-related standards that are widely-used in biomedical research and related activities.

CASC-2014 BD2K: Facilitating the broad use of data 19 Making Data Usable (cont.) 2. Frameworks for Community-Based Standards Efforts: Establish a framework of policies, governance, administrative procedures, and funding to routinely support community-based standards efforts, and Use that framework to provide catalytic support for particularly opportune efforts under BD2K that are broadly relevant to biomedical research. Making data Discoverable o Development of an NIH BD2K Data Discovery Index Coordination Consortium

CASC-2014 Creating the connected biomedical digital research enterprise 20 Digital Assets; o The research assets that were once physical – lab notebooks on the shelf, images as hardcopy, software as punched cards, journals as hardcopy, etc., are now digital. o Include data (of various types), software, workflows, publications, and more, not only increase the pace of the scientific process, but also allow connections to be made and patterns to be discovered that were previously hidden.

CASC-2014 Biomedical Research as a Connected Digital Enterprise 21 To do: o Expanding metrics of scientific productivity beyond publications o Supporting Reproducible Science o Increasing productivity and reducing costs while supporting increased creativity and impact o Improved interoperability o Advancing analysis and modeling o Supporting a new work force

NIGMS: Investing in Discovery Division Overview: