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STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies

Iain Hepburn12, Weiliang Chen2, Stefan Wils12 and Erik De Schutter12*

Author Affiliations

1 Theoretical Neurobiology, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, Wilrijk,2610, Belgium

2 Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Seaside House, 7542, Onna, Onna-son, Kunigami, Okinawa 904-0411, Japan

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BMC Systems Biology 2012, 6:36  doi:10.1186/1752-0509-6-36

Published: 10 May 2012

Additional files

Additional file 1:

Gillespie Stochastic Simulation Algorithm (SSA), optimizations and implementations in STEPS. A description of the algorithms and optimizations used in STEPS solvers Wmdirect and Tetexact [66,67].

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Additional file 2:

Subvolume Size. An analysis of acceptable tetrahedron size range for reaction-diffusion simulations in STEPS.

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Additional file 3:

Cubic and Tetrahedral mesh comparison. A statistical comparison between cubic and tetrahedral mesh representation of five different dendritic spine geometries.

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Additional file 4:

Validation. Detailed descriptions of the validation models used in this study, along with statistical analysis of results from STEPS simulations. [68].

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Additional file 5:

Simulator Efficiency Test Model. A description of the model used to study efficiency of STEPS, MesoRD and Smoldyn, along with model files for each simulator.

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Additional file 6:

Figure S1. SBML Test Suite support. All 980 models (l3v1) of the SBML Test Suite 2.0.0 (as of 2011/06/01) were imported, run in the Wmrk4 deterministic solver in STEPS and results compared against given solutions. The chart shows the proportion of models supported (red) and unsupported (other colors). The unsupported models are separated into 4 categories.

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