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

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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

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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.

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NIGMS Budget Percentage Share by Mechanism FY 2013 Appropriation

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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

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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

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• 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.

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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

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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.

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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

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• 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

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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

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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)

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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

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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

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• 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.

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BD2K: Facilitating the broad use of data

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• 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

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• 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

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• 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