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TR& D Project 4

TR& D Project 4. Michael Blinov Jeff Dutton Fei Gao Anuradha Lakshminaranaya Ye Li Frank Morgan Igor Novak Oliver R ü benacker Dan Vasilescu. Ion I. Moraru James C. Schaff. Application Development. Work that is presented in more detail elsewhere

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TR& D Project 4

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  1. TR&D Project 4 • Michael Blinov • Jeff Dutton • Fei Gao • Anuradha Lakshminaranaya • Ye Li • Frank Morgan • Igor Novak • Oliver Rübenacker • Dan Vasilescu • Ion I. Moraru • James C. Schaff Application Development

  2. Work that is presented in more detail elsewhere GUI “polishing” (better error messages, more inline info, auto-complete, etc.) Enhanced geometry interface (segmentation support, primitives wizard, ROI goodies) New solver deployments New external database links (Pathway Commons) New pathway search/import functionality (SyBiL integration) Enhanced metadata and annotation support Compute server upgrades New backup and archival infrastructure VFRAP standalone application Grid Initiative Re-purposing older, decommissioned cluster UCHC OSG site operational Production work since 9/09 VCell OSG layer prototype design Enhanced VCell “Application” From global parameters to application parameters… Application-level output functions (simulation post-processing) New “pre-math” combined editor pane Reaction kinetics override Application-level user-defined functions Application-level user-defined equations Summary

  3. The Open Science Grid Initiative • Site build ramped up in January of 2009 • 58 CPU cluster running Rocks Clusters operating system • Theoretically 1,392 CPU hours available for production daily • Only site known to us to have OSG Production Compute Element running on a Microsoft Active Directory integrated Linux cluster • Our unique architecture has caused problems and brought us added attention from OSG resources to overcome these issues and to improve the OSG software stack • Site registered with OSG in February 2009 • Site name is UCHC_CBG • Doing production in September 2009

  4. The Open Science Grid Initiative Production – Job Counts Production - Cumulative • More than 16 production users have run jobs • More than 30,000 compute hours of production • Average about 228 hours of production per day • Engage (OSG generic VO) is biggest user • Average about 182 jobs per day • SBGrid is ramping up and expected to be a heavy user • New CompBioGrid user from Storrs will be prototyping a grid application on UCHC_CBG in the coming weeks

  5. Physiology Molecules Structures (topology) Reactions Fluxes Applications Structure mapping (topology to geometry) Initial Conditions Boundary conditions Diffusion constants (if spatial) Electrophysiology protocols Enable/disable reactions Fast reactions Model analysis Stochastic rate conversion Applications Structure mapping (topology to geometry) Initial Conditions Boundary conditions Diffusion constants (if spatial) Electrophysiology protocols Enable/disable reactions Fast reactions Model analysis Stochastic rate conversion Applications Structure mapping (topology to geometry) Initial Conditions Boundary conditions Diffusion constants (if spatial) Electrophysiology protocols Enable/disable reactions Fast reactions Model analysis Stochastic rate conversion Simulations Timecourse Timestep Mesh size Solver type Solver settings Parameter changes Parameter scans Parameter sensitivity Simulations Timecourse Timestep Mesh size Solver type Solver settings Parameter changes Parameter scans Parameter sensitivity Simulations Timecourse Timestep Mesh size Solver type Solver settings Parameter changes Parameter scans Parameter sensitivity Results Results Results Mathematical Description (view-only, automatically generated) Mathematical Description (view-only, automatically generated) Mathematical Description (view-only, automatically generated)

  6. Enhanced VCell Application

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