Distributed Cell Biology Simulations with E-Cell System

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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...
Masahiro Sugimoto, Kouichi Takahashi, Tomoya Kitay
Added 02 Jul 2010
Updated 02 Jul 2010
Type Conference
Year 2004
Authors Masahiro Sugimoto, Kouichi Takahashi, Tomoya Kitayama, Daiki Ito, Masaru Tomita
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