Scientific Computing Seminar

Date:

Monday, March 1, 2004

Time:

11:00am-12:00pm

Location:

50B-6208

Seminar Speaker:

Jian He
Dept. of Computer Science
Virginia Polytechnic Institute

Title:

Global Parameter Estimation for Cell Cycle Modeling in Systems Biology

Abstract:

Cell cycle models for Eukaryotes in systems biology are very complex, involving many unknown parameters in the ODE system and multiple local minima in the design domain. Local gradient-based methods fail to completely explore the global parameter space. We propose a novel parameter estimation approach to effectively attack the problem by combining a local gradient-based method with a global optimization algorithm---DIRECT. Although several sequential implementations for this algorithm have been successfully applied to large scale MDO problems, few parallel versions of the DIRECT algorithm have addressed well algorithm characteristics such as a single starting point, an unpredictable workload, and a strong data dependency. These challenges engender many interesting design issues including domain decomposition, data access and management, and workload balancing. In the present work, a hierarchical parallel scheme has been developed to address these challenges at three levels supported by dynamic process management, mixed programming models, and parallel/distributed data structures. Results for numerical simulations and performance measurements on a frog egg model and two test functions were obtained on a 200 node Linux cluster.

Sponsor of Seminar:

Chris Ding

Scientific Computing

Contact Esmond G. Ng EGNg@lbl.gov