Emmet Caulfield

Cellmc: an Sbml Model Compiler for Cell/be and X86 Emmet Caulfield

In silico simulation of chemical reactions is playing an increasingly important role in understanding cellular biochemistry, simulating in vivo processes such as genetic and enzymatic action, and giving rise to the field of computational systems biology. The Systems Biology Markup Language (SBML) provides a standard way to describe models of biochemical reaction networks, and the Stochastic Simulation Algorithm (SSA) is an effective and popular method for simulating systems with many reacting species, which cannot be simulated using numerical solution techniques whose time-complexity grows exponentially with number of chemical species. This book describes CellMC, an open source program generator based on XML Stylesheet Language Transformation (XSL-T) that produces a fully vectorized and parallelized executables realising SSA for any homogeneous biochemical model expressed as SBML. The compiler works on a variety of Cell/BE and Intel/Linux platforms, including a PlayStation 3 cluster. The Intel/Linux executables produced are shown to outperform others in the literature by a considerable multiple.