Computational Sciences within NIGMS
Protein Ontology Meeting, Georgetown, June 18, 2014
Veerasamy “Ravi” Ravichandran, Ph.D. Program DirectorBiomedical Technology, Bioinformatics and Computational BiologyNIGMS/NIH
CASC-20142
National Institutes of Health
2
NationalLibrary of Medicine
National Center forAdvancing
Translational Science
NationalInstitute of
NursingResearch
NationalInstitute of
NeurologicalDisorders
and Stroke
National Institute on
MinorityHealth and
HealthDisparities
Clinical Center
Center forScientificReview
Center forInformationTechnology
National Center for
Complementaryand Alternative
Medicine
National Institute on
Drug Abuse
National Institute of EnvironmentalHealth Sciences
National Institute of
General Medical Sciences
National Institute of Diabetes and
Digestive andKidney Diseases
National Institute on Deafnessand Other
Communication Disorders
Eunice Kennedy Shriver
National Institute of
Child Healthand Human
Development
National Institute of
BiomedicalImaging and
Bioengineering
National Institute of Mental Health
National Institute of
Dental andCraniofacial
Research
NationalCancer Institute
NationalEye Institute
NationalHeart, Lung,
and Blood Institute
NationalHuman Genome
Research Institute
NationalInstituteon Aging
National Instituteon Alcohol Abuse and Alcoholism
National Institute of Allergy and
Infectious Diseases
National Institute of Arthritis andMusculoskeletal
and Skin Diseases
Office of the Director
John E. FogartyInternational
Center for Advanced
Study in theHealth Sciences
27 Institutes and Centers
CASC-2014
NIGMS Organizational Chart
3
Office of the DirectorJon R. Lorsch, Ph.D.Director
Office of Administrative ManagementSally Lee, Chief
Office of Communications and Public LiaisonAnn Dieffenbach, Chief
Office of Program Analysis and EvaluationPaul Sheehy, Ph.D.Acting Chief
Office of Scientific ReviewHelen Sunshine, Ph.D. Chief
Division of Biomedical Technology,Bioinformatics, and Computational BiologySusan Gregurick, Ph.D.Director
Division of ExtramuralActivitiesAnn Hagan, Ph.D.Director
Division of Cell Biology and BiophysicsCatherine Lewis, Ph.D. Director
Division of Genetics and Developmental BiologyJudith H. Greenberg, Ph.D. Director
Division of Training, Workforce Development, and DiversityAlison Hall, Ph.D.Acting Director
Division of Pharmacology, Physiology, andBiological ChemistryMichael Rogers, Ph.D.Director
Office of Emergency Care ResearchJeremy Brown, M.D. Director
v
vBiomedical Technology Branch vBioinformatics and Computational Biology Branch
CASC-20144
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-20145
NIGMS Budget Percentage Share by Mechanism FY 2013 Appropriation
5
RPGs58%
SBIR/STTR3%
centers19%
Other Re-
search7%
Training8%
R&D Contracts2%
RMS3%
Intramural0%
FY 2014 NIGMS budget: 2.359 billion
RPGs: R00 R01 R15 R21 R37 P01 DP1 DP2 U01
CASC-20146
Targeted support for specific areas of research increased during the budget doubling
Jim Deatherage, NIGMS
CASC-20147
Biomedical Technology, Bioinformatics and Computational Biology Division
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-20149
Biomedical Technology, Bioinformatics and Computational Biology Research Enterprise
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-201410
Biomedical Technology, Bioinformatics and Computational Biology Research Enterprise
Computational and Systems BiologyNew approaches, algorithms and methods for an integrative understanding of complex biological processes
Mathematical and Statistical ModelingPromote research at the interface of the biological and mathematical sciences.
MIDAS - Modeling of Infectious Disease Agent StudyCollaborative research to model the dynamics of infectious diseases
Data SciencesNew shared computing algorithms and bioinformatics methods to manage, visualize and analyze complex scientific data, including standards and ontology
CASC-201411
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-201412
Resource for Analysis, Visualization, and Integration of Networks (RAVIN)
• P41 funding mechanism
• PI: Trey Ideker, UCSD
• Data-driven Scienceo 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-201414
BBCB Partnerships
• 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-201415
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.
http://www.bisti.nih.gov (Susan Gregurick, Director, BBCB)
CASC-201416
New BISTI Funding Opportunities
• Early Stage Development of Technologies in Biomedical Computing,
Informatics, and Big Data Science (R01) PA-14-155 and (R43/R44) PA-
14-154
• 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-201417
New BISTI Funding Opportunities
• Extended Development, Hardening and Dissemination of Technologies in Biomedical Computing, Informatics and Big Data Science (R01) PA-14-156 and (R41/R42) PA-14-157
• 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
oRecommending 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;
oThe 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:
oExpanding metrics of scientific productivity beyond
publications
oSupporting Reproducible Science
o Increasing productivity and reducing costs while
supporting increased creativity and impact
o Improved interoperability
oAdvancing analysis and modeling
oSupporting a new work force
NIGMS: Investing in Discovery
Division Overview: www.nigms.nih.gov/About/Overview/bbcb.htm