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Open Access Software

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

Brian Drawert1, Stefan Engblom23 and Andreas Hellander1*

Author Affiliations

1 Department of Computer Science, University of California, Santa Barbara, California 93106, USA

2 Department of Information Technology, Uppsala University, Uppsala 75105, Box 337, Sweden

3 UPMARC, Uppsala Programming for Multicore Architectures Research Center, Uppsala, Sweden

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BMC Systems Biology 2012, 6:76  doi:10.1186/1752-0509-6-76

Published: 22 June 2012

Additional files

Additional file 1:

urdme.tar.gz. The current release of URDME. Also available for download via http://www.urdme.org. webcite

Format: GZ Size: 1.9MB Download file

Open Data

Additional file 2:

minsweep.tar.gz. Model files required to run the first example in the main paper.

Format: GZ Size: 61KB Download file

Open Data

Additional file 3:

benchmark.tar.gz. Model files required to run the second example in the main paper.

Format: GZ Size: 117KB Download file

Open Data

Additional file 4:

neuron.tar.gz. Model files required to run the third example in the main paper.

Format: GZ Size: 1.4MB Download file

Open Data

Additional file 5:

urdme_sbml_converter.tar.gz. SBML conversion tool to create URDME model files from a SBML model file describing chemical reactions.

Format: GZ Size: 25KB Download file

Open Data

Additional file 6:

validation.pdf. Simulation results for a simple diffusion problem on the surface of a sphere and for the Min system [8,34,55,56,59,60].

Format: PDF Size: 232KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7:

urdme_software_comparision.tar.gz. Model files and scripts used to conduct the performance benchmark in the discussion section and the simulations described in Additional file 6.

Format: GZ Size: 7.1MB Download file

Open Data