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NIH / NIGMS Perspective

NIH / NIGMS Perspective. Karin A. Remington, Ph.D., NIGMS NCSA S trategic Planning Meeting April 20, 2010. First Genome Sequenced 1995 Haemophilus influenzae 1.8 million basepairs. Meta-Genomics Pilot Study:.

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NIH / NIGMS Perspective

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  1. NIH / NIGMS Perspective Karin A. Remington, Ph.D., NIGMS NCSA Strategic Planning Meeting April 20, 2010

  2. First Genome Sequenced 1995 Haemophilus influenzae 1.8 million basepairs

  3. Meta-GenomicsPilot Study: The Sargasso SeaDescribed in: Venter et al. Environmental Genome Shotgun Sequencing of the Sargasso Sea, Science 304, 66-74 (2004)

  4. Sorcerer ll ExpeditionSampling Sites

  5. Sorcerer GOS Expedition34 sites, baseline of 150,000 sequences site Just outside Canadian water Browns bank Outside Halifax Bedford Basin Bay of Fundee Transit outside of Maine Newport Harbor, Rhode Island Block Island Cape May Next To Nuke Power Plant in Delaware Bay Chesapeake Bay near Annapollis 11.3 miles off of Nags Head N.C. South of Charleston S.C Off Dry Tortugas Northwest of western most Cuba Yucatan Channel, Mexico Carribean Sea 30 nm of Rosario bank, Honduras 80 nm north of Panama Canal Borro de Colorado at STRI, Panama 35 miles off of Panama City 250 miles from Panama Canal 30 miles from Coco's Island, Ecuador Dirty Rock Coco's Island, Ecuador Devil's Crown Off of Floreana, Galapagos Off theCoast of Floreana, Galapagos Espumilla Beach, Santigo Island, Galapagos Thermal Vent Roca Redonda, Galapagos Off Fernandina Island, Galapagos Floreana Flamingo Pond, Galapagos North Seamore Island, Galapagos Wolf Island, Galapagos Cabo Marshall, Isabella Island Galapagos

  6. Challenges • Scalability (both memory and I/O) • Flexible components, with incremental, fault tolerant design • Standardization so that studies can build upon one another • Changing definitions over time • Visualization and usability

  7. Comparative analyses of assemblies GS05 GS04 GS06 GS02 GS03 GS08 GS07 GS09 GS10 GS00 GS14 GS25 GS01 GS31 GS16 GS15 GS34 GS29 GS27 GS30 GS21 GS22 GS19 GS17 GS23 North Atlantic

  8. Flamingo Pond (Galapagos) Panama Canal Eastern US Seaboard Gulf Stream Galapagos Sargasso Sea and Yucatan Channel, Mexico North Atlantic Comparative analyses of assemblies

  9. Comparative analyses of gene variationExample: proteorhodopsin Plus 23 additional pages….

  10. Comparative analyses of gene variationExample: proteorhodopsin 2 R01 GM 76667 5

  11. 21st Century Challenges for NIH • Revolutionary and rapid changes in Science • Increasing breadth of mission and growth • Complex organization with many units(27 institutes and centers, multiple program offices, e.g., OWHR, OAR, ORD, ...) • Structured by Disease, Organ, Life stage, Disciplines …. • Rapid Convergence of Science

  12. NIH: Many Compute Intensive Programs: • NIGMS Systems Biology Centers • NCI Integrative Cancer Biology Program • National Centers for Biomedical Computing (“Roadmap”) • Intramural Systems Biology – NIAID, e.g. • Coordinated Clinical Research Opportunities (via CTSAs, e.gg.) • Various other programs… decentralized, nascent, constantly in review

  13. Models of Infectious Disease Agent Study Computational and mathematical investigations of: • Dynamics of emergence and spread of pathogens and their products • Identification and surveillance of infectious diseases • Effectiveness and consequences of intervention strategies • Host/pathogen interactions • Ecological, climatic, and evolutionary dimensions of infectious diseases outbreaks.

  14. National Centers for Biomedical Computing (NCBCs) • Development of cutting edge computer science • Translation of this computer science into biomedical computation, i.e., effective algorithms and environments for solving real biological problems • Enable the analysis, modeling, understanding, and prediction of dynamic and complex biomedical systems across time and distance scales • Allow the integration of biomedical and behavioral data and knowledge at all levels of organization

  15. Some NCBC Grand Challenges: • Automated shape analysis • Knowledge resources that enhance experimentation • Integration of bioinformatics data and tools • High-throughput sample acquisition, analysis and identification • Relationship between genomic and clinical data • Multi-body dynamic simulation, modeling and structural analysis

  16. See detailed center information at http://ncbcs.org

  17. Genes Cellstructure-function Tissuestructure-function Organstructure-function Clinical medicine mRNA Proteins Lipids Carbohydrates … 4 tissue types 30,000+ genes 100,000+proteins 200+ cell types 12 organsystems 1 body Courtesy of Peter Hunter MultiscaleModeling Spanning scales from molecular to population, designed to illuminate biological processes and further the predictive capability in biological, biomedical and environmental systems. Multi-scale modeling encompasses concepts of space, time and state space. Biological Scales

  18. IMAG Multiscale Modeling (MSM) Consortium Working Groups WG1 - Filament Dynamics and Simulation (FDS) WG2 - Cardiac and Skeletal Muscle Physiology WG3 - Macro-To-Micro Scale Transport in Human Systems WG4 - Cell Level Modeling WG5 - High Performance Computing, Computational Issues and Algorithms WG6 - Tissue Mechanics WG7 - Multiscale Imaging WG8 – Theoretical Methods WG9 – Nano-modeling WG10 – Model Sharing

  19. The CHALLENGES of finding funding at the NIH

  20. A portrait of NIH Study Sections, when it comes to interdisciplinary teams and emerging areas:

  21. To encourage fair review of the desired collaborations: Special Emphasis Panels, for targeted FOAs Multiple PI applications Encouragement of “New” Investigators, with IC-level policies to boost likelihood of funding “Enhancing Peer-Review” effort underway

  22. NIH: some recent activities • NIH-wide IT infrastructure assessment • NHGRI Cloud Computing workshop • NCI/NIGMS Synthetic Biology workshop • NHGRI Informatics and Analysis strategic planning • National Centers for Biomedical Computing competitive renewal

  23. Eric Green account: Sequencing Bioinformatics

  24. Enabling biology: We really need: to carefully design, document, and scrutinize experiments to test hypotheses and avoid misinterpreting collected data to rely less on automated annotation, and more on focused studies, and then create tools to assist to integrate intra-organism and intra-community systems biology as well as hypothesis-generating and hypthothesis-testing systems biology

  25. Human polymorphism

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