University of Michigan

Director: Dr. Brian Athey

Email Dr. Donald Jenkins at NLM /NIH; Phone: 301-435-3273

EVENT FLYER in pdf format: Click here

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Event Title “Computational Systems Biology to Accelerate Research in Complex Disease Applications: 1) Cellular mechanisms of oxidative damage in Diabetes Mellitus complications; and 2) Prostate Cancer ”
Description Tutorial sessions with follow-on discussions given by NCIBI senior scientists and selected collaborators using methods of Computational Systems Biology as applied to complex diseases. Applications foci on 1) problems in cellular mechanisms of oxidative damage in Diabetes Type I complications; and 2) Prostate Cancer. Emphasis will be on learning about and using NCIBI (and partners’) software, tools, modeling capabilities, and data resources for discovery and problem solving applied to complex diseases using an NCBC-wide interoperable workflow scaffold.
Date July 19, 2006
Time 9:00 a.m. - 12:00 noon with optional follow-on lunch at Natcher Cafeteria for continued discussions with NCIBI representatives
Location

NIH Campus, Bethesda MD
Natcher Conference Center (Lower Level), Room F1/F2
NIH Host NCIBI NIH Lead Science Officer, Dr. Donal Jenkins NLM/NIH and Program Officer, Dr. Karen Skinner, NIDA/NIH
Targeted Audience NIH intramural and extramural researchers, NIH special interest groups, including clinical and translational scientists; other scientists interested in applications to computational approaches to understanding complex biological systems.
Participants

Brian D. Athey*, H.V. Jagadish*, Matthias Kretzler*, Gilbert S. Omenn*, Jignesh Patel*, David J. States*, Peter Woolf*, Scott Tomlins*, Jill Mesirov and Michael Reich+, and Robert F. Murphy†

*University of Michigan, +Broad Institute, †Carnegie Melon University
Agenda 9:00 a.m.-10:00 a.m. Interoperable software architecture and tools for systems biology with applications I

Session Goals:
• Present a vision for a collaborative web services- based software architecture allowing modules and tools developed at multiple centers to interoperate;
• Introduction to NCIBI framework, tools, and databases to understand biological systems:

o Integrated problem solving software environment: GenePattern (Broad), geWorkbench (with MAGNet Center), and Taverna (EBI)
o Michigan Molecular Interactions (MiMI) and pathways database
o Molecular interactions data integration
o SAGA subgraph in-exact matching tool

Application Domain Example:
• Recapitulating the discovery of TMPRSS2/ETV gene fusions in prostate cancer

10:00 a.m. - 10:15 a.m. Discussion
10:15 a.m.-10:30 a.m. Break
10:30 a.m. - 11:30 a.m. Interoperable software architecture and tools for systems biology with applications II

Session Goals: Introduce users to additional NCIBI tools and capabilities

o Novel Natural Language Processing to enhance graph analysis of complex disease
o Bayesian network analysis of signaling pathway
o Gene Expression Analysis and transcriptional regulatory network: Examples in Prostate Cancer and in cellular mechanisms
o Discuss implementation issues, coordination and strategies

Application Domains Examples:
• Applied deep literature mining and enhanced information retrieval: Wnt signaling Pathway example
• Bayesian network analysis of signal transduction pathways in Prostate Cancer
• Inference of regulatory motifs form gene expression data and modeling in Diabetes complications
11:30 a.m. - 12:00 noon Discussion
12:00 noon - 1:30 p.m.

Optional follow-on lunch (on your own) at Natcher Cafeteria for continued discussions with NCIBI representatives

Event Website http://www.ncibi.org/center-news/ncibi-tutorial-session-on-computational-systems-biology-at-the-ncbc-ahm-july-19-2006-nih-campus-bethesda-md
Accessibility Needs  Individuals with disabilities who need sign language interpreters and/or reasonable accommodation to participate in this event should contact Jennifer Villani at 301-451-6446 or villanij@mail.nih.gov or through the Federal Relay 1-800-877-8339. Requests should be made at least five days in advance of the meeting.