Biomedical Computation

at NIH

Michael Marron

National Center for Research Resources

National Institutes of Health

Current NIH Activities International networks for biomedical data & software sharing: caBIG

(NIH/NCI), BIRN (NIH/NCRR)• National Health Information Network support w/ HHS/ONCHIT NIH Roadmap National Centers for Biomedical Computing (NCBCs)• Cancer Imaging and Computational Centers• Modeling of Infectious Disease (MIDAS) Bioinformatics Resource Centers for Emerging and Re-emerging

Infectious Disease• Proteomics and Protein Structure Initiatives P41 Computational Centers – eleven exist, on tools &

cyberinfrastructure• National Library of Medicine information & analysis servers• Many Investigator Research Grants contain supercomputing support Interdisciplinary Centers• [more]

fMRI

Clinical Query

Integrated View

Receptor Density

Web

Other Databases

Structure

Clinical

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ARIP - 20MG ARIP - 30MG RISP - 06MG PLACEBOTreatment Group

MediatorMediator

BIRN NetworkBIRN Network• Infrastructure that facilitates distributed collaborations in biomedical

science• Sharing data and tools: data grid and computational grid• Initial focus in brain imaging of neurological disorders (human and mice) • 31 Universities, 39 Research Groups, connected through Internet2

http://www.nbirn.net/

Physics-based Simulation of Biological Structures (SIMBIOS)PI: Russ Altman, MD, PhD PI Institution: Stanford University

This Center will develop, disseminate, and support a simulation tool kit (SimTK) that will enable biomedical scientists to develop and share accurate models and simulations of biological structures from atoms to organisms. SimTK will be an open-source, extensible, object-oriented framework for manipulating data, models, and simulations. The software will include advanced capabilities for modeling the geometry and physics of biological systems, generating the governing differential equations of these systems, integrating the equations to simulate the system dynamics, and interpreting the simulation results through comparison with experimental data.

Informatics for Integrating Biology and the Bedside (I2B2)PI: Isaac Kohane, MD, PhDPI Institution: Brigham and Women's Hospital

The I2B2 Center is developing a scalable informatics framework that will bridge clinical research data and the vast data banks arising from basic science research in order to better understand the genetic bases of complex diseases. This knowledge will facilitate the design of targeted therapies for individual patients with diseases having genetic origins.

National Alliance for Medical Imaging Computing (NAMIC)PI: Ron Kikinis, MDPI Institution: Brigham and Women's Hospital

NAMIC’s goal is to develop, integrate, and deploy computational image analysis systems that are applicable to multiple diseases, in different organs. To provide focus for these efforts, a set of key problems in schizophrenia research has been selected as the initial Driving Biological Projects (DBPs).

The CCB develops, implements, and tests computational biology methods that are applicable across spatial scales and biological systems. The Center focuses on the brain, specifically on neuroimaging, and involves research in mathematics, computational methods and informatics. It also is involved in the development of a new form of software infrastructure – the computational atlas – to manage multidimensional data spanning many scales and modalities.

Center for Computational Biology (CCB)PI: Arthur Toga, PhDPI Institution: University of California at Los Angeles

NCIBI develops and interactively integrates analytical and modeling technologies to acquire or create context-appropriate molecular biology information from emerging experimental data, international genomic databases, and the published literature.

The NCIBI supports information access and data analysis workflow of collaborating biomedical researchers, enabling them to build computational and knowledge models of biological systems validated through focused work on specific diseases.

PI: Brian Athey, PhD

Pi Institution: University of Michigan

PI: Andrea Califano, PhDPI Institution: Columbia University

Construct an environment for comprehensive mapping and analysis of molecular cellular interactions

• Evidence integration framework to collect and fuse diverse cellular interaction clues based on statistical relevance

• Comprehensive set of physics- and knowledge-based methodologies to fill framework

• Methodologies and filters, anchored in formal domain ontologies, to associate specific interactions to an organisms, tissue, molecular, and cellular context

A consortium of biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form.

PI: Mark A. Musen, MD, PhDPI Institution: Stanford University

Open Biomedical Ontologies

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Open Biomedica

l Data (OBD)

BioPortal

Capture and index experimental results

Revise biomedical

understanding

Relate experimental data to

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PI: Ary GoldbergerPI: Ary Goldberger

http://www.sci.utah.edu/cibc/

PI: Chris Johnson

http://www.ks.uiuc.edu/ http://www.ks.uiuc.edu/ PI: Klaus SchultenPI: Klaus Schulten

http://www.nrcam.uchc.edu/ http://www.nrcam.uchc.edu/

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PI: Arthur TogaPI: Arthur Toga

Carolina Center for Exploratory Genetic AnalysisURL: http://www.renci.org/research/ccega/

PI: Dan Reed

Computation Center for Biomolecular ComplexesURL: http://ncmi.bcm.tmc.edu/ccbc

Funding OpportunitiesGeneral Funding Information: http://www.bisti.nih.gov/bistic_funding.cfm

Collaborations with National Centers for Biomedical Computing - PAR-05-063 Mechanism: R01 Receipt Dates: Jan 17 and May 17, 2006

Continued Development and Maintenance of Bioinformatics and Computational Biology Software - PAR-05-057

Mechanism: R01, Supplements Receipt Date: May 17, 2006 Innovations in Biomedical Computation Science and Technology - PAR-03-106

Mechanisms: R21/R33, R01 Receipt Date: Feb 26, 2006 NLM Research Grants in Biomedical Informatics and Bioinformatics - PA-06-094

Mechanism: R01 Receipt Dates: Feb 1 and Jun 1, 2006Shared Instrumentation Grant program - PAR-06-093

Mechanism: S10 Receipt Date: Mar 22, 2006 (electronic!)Mentored Quantitative Research Development Award - PA-06-087

Mechanism: K25 Receipt Dates: Feb 1 and Jun 1, 2006Innovations in Biomedical Computational Science and Technology: SBIR/STTR Initiative - PAR-06-088 & PAR-06-089

Mechanisms: R41/2/3/4 Receipt Date: Feb 26, 2006 (electronic!) Integration of Heterogeneous Data Sources - PA-06-010 & PA-06-011

Mechanisms: R41/2/3/4 Receipt Date: Apr 1 2006 (electronic!)

More on Funding Opportunities

Advanced Proteomic Platforms and Computational Sciences for the NCI Clinical Proteomic Technologies Initiative - RFA-CA-07-005

Mechanisms: R01, R21, R21/R33 Receipt Date: Apr 11, 2006 Structural Genomics Knowledgebase - RFA-GM-06-004

Mechanism: U01 Receipt Date: Feb 23, 2006 Training in Computational Neuroscience: From Biology to Model and Back Again - RFA-DA-06-010

Mechanism: T90 Receipt Date: Mar 13, 2006 NIH Support for Conferences and Scientific Meetings - PA-06-041

Mechanisms: R13/U13 Receipt Dates: Apr 15, 2006 (electronic!)

Search all funding opportunities: http://grants.nih.gov/grants/guide/index.html

Electronic Submission Information: http://era.nih.gov/ElectronicReceipt Mac Support: http://www.grants.gov/MacSupportTraining: http://era.nih.gov/ElectronicReceipt/training.htm#1

Electronic Submission: http://www.grants.gov/