Stochastic reaction-diffusion simulation with MesoRD

Authors:
Johan Hattne;David Fange;Johan Elf
Affiliations:
Department of Cell and Molecular Biology, BMC, Uppsala University 75124 Uppsala, Sweden;Department of Cell and Molecular Biology, BMC, Uppsala University 75124 Uppsala, Sweden;Department of Cell and Molecular Biology, BMC, Uppsala University 75124 Uppsala, Sweden
Venue:
Bioinformatics
Year:
2005

Citing 0
Cited 8

Performance evaluation comes to life: quantitative methods applied to biological systems

ACM SIGMETRICS Performance Evaluation Review
An adaptive algorithm for simulation of stochastic reaction-diffusion processes

Journal of Computational Physics
Modelling spatial heterogeneity and macromolecular crowding with membrane systems

CMC'10 Proceedings of the 11th international conference on Membrane computing
Flexible single molecule simulation of reaction-diffusion processes

Journal of Computational Physics
Research article: Abstract Next Subvolume Method: A logical process-based approach for spatial stochastic simulation of chemical reactions

Computational Biology and Chemistry
Simulation strategy of membrane computing to characterize the structure and non-deterministic behavior of biological systems: a case study with ligand-receptor network of protein TGF-β

IVIC'11 Proceedings of the Second international conference on Visual informatics: sustaining research and innovations - Volume Part I
Analyzing the distribution of threshold voltage degradation in nanoscale transistors by using reaction-diffusion and percolation theory

Journal of Computational Electronics
Simulation of Spatial P system models

Theoretical Computer Science

Quantified Score

Hi-index	3.85

Visualization

Abstract

Summary: MesoRD is a tool for stochastic simulation of chemical reactions and diffusion. In particular, it is an implementation of the next subvolume method, which is an exact method to simulate the Markov process corresponding to the reaction-diffusion master equation. Availability: MesoRD is free software, written in C++ and licensed under the GNU general public license (GPL). MesoRD runs on Linux, Mac OS X, NetBSD, Solaris and Windows XP. It can be downloaded from http://mesord.sourceforge.net. Contact:johan.elf@icm.uu.se; johan.hattne@embl-hamburg.de Supplementary information: 'MesoRD User's Guide' and other documents are available at http://mesord.sourceforge.net.