%0 Journal Article
%T STEPS: efficient simulation of stochastic reaction¨Cdiffusion models in realistic morphologies
%A Iain Hepburn
%A Weiliang Chen
%A Stefan Wils
%A Erik De Schutter
%J BMC Systems Biology
%D 2012
%I BioMed Central
%R 10.1186/1752-0509-6-36
%X We describe STEPS, a stochastic reaction¨Cdiffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction¨Cdiffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation.STEPS simulates models of cellular reaction¨Cdiffusion systems with complex boundaries with high accuracy and high performance in C/C++, controlled by a powerful and user-friendly Python interface. STEPS is free for use and is available at http://steps.sourceforge.net/ webciteAs the understanding of the molecular systems governing many aspects of cellular function improves it is becoming increasingly clear that the assumption of mass action kinetics in well-mixed volumes is often invalid. A good example is calcium signaling, which can be highly localized with very steep concentration gradients [1-3]. Calcium signaling depends on the interaction between membranes where the calcium channels are located and the cytoplas
%U http://www.biomedcentral.com/1752-0509/6/36