Distributed Cell Biology Simulations with E-Cell System

Many useful applications of simulation in computational cell biology, e.g. kinetic parameter estimation, Metabolic Control Analysis (MCA), and bifurcation analysis, require a large number of repetitive runs with different input parameters. The heavy requirements imposed by these analysis methods on computational resources has led to an increased interest in parallel- and distributed computing technologies. We have developed a scripting environment that can execute, and where possible, automatically parallelize those mathematical analysis sessions transparently on any of (1) single-processor workstations, (2) Shared-memory Multiprocessor (SMP) servers, (3) workstation clusters, and (4) computational grid environments. This computational framework, E-Cell SessionManager (ESM), is built upon E-Cell System Version 3, a generic software environment for the modeling, simulation, and analysis of whole-cell scale biological systems. Here we introduce the ESM architecture and provide results f...

• Type: Conference
• Year: 2004
• Where: LSGRID
• Authors: Masahiro Sugimoto, Kouichi Takahashi, Tomoya Kitayama, Daiki Ito, Masaru Tomita
• Keywords: Computational Cell Biology, Distributed And Parallel Computing, Kinetic Parameter Estimation, LSGRID 2004, Parameter Estimation