CellMC : An XSLT-based SBML Model Compiler for Cell/BE and IA32

Abstract: In-silico simulation of chemical reactions is playing an increasingly important rôle in furthering understanding of cellular biochemistry, simulating in-vivo chemical reactions such as genetic and enzymatic action, and giving rise to the field of computational systems biology. The Systems Biology Markup Language (SBML) has been defined to provide a standard way to describe models of biochemical reaction networks, and the Stochastic Simulation Algorithm is an effective and popular method for simulating systems with many reacting species, which cannot be simulated using most numerical solution techniques whose time-complexity grows exponentially with number of chemical species. CellMC, an open source program generator based on XML Stylesheet LanguageTransformation (XSL-T), is presented and evaluated. It produces a SIMD-ised and parallelised executable realising SSA for any homogeneous biochemical model expressed as SBML. The compiler works on a variety of Cell/BE and IA32 platforms, including a Sony PlayStation 3 cluster. The IA32 executables produced are shown to outperform others in the literature by a considerable multiple, and they, in turn, are outperformed by those on Cell/BE.