Multiscale reaction-diffusion simulations with Smoldyn

Journal article

Summary: Smoldyn is a software package for stochastic modelling of spatial biochemical networks and intracellular systems. It was originally developed with an accurate off-lattice particle-based model at its core. This has recently been enhanced with the addition of a computationally efficient on-lattice model, which can be run stand-alone or coupled together for multiscale simulations using both models in regions where they are most required, increasing the applicability of Smoldyn to larger molecule numbers and spatial domains. Simulations can switch between models with only small additions to their configuration file, enabling users with existing Smoldyn configuration files to run the new on-lattice model with any reaction, species or surface descriptions they might already have.
Availability and Implementation: Source code and binaries freely available for download at www.smoldyn.org, implemented in C/C++ and supported on Linux, Mac OSX and MS Windows.
Contact:[email protected]
Supplementary Information: Supplementary data are available at Bioinformatics online and include additional details on model specification and modelling of surfaces, as well as the Smoldyn configuration file used to generate Figure 1.

Authors: Robinson, M; Andrews, S; Erban, R

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Oxford University Press
• Journal: Bioinformatics
• Volume: 31
• Issue: 14
• Pages: 2406–2408
• Publication date: 2015-03-18
• Acceptance date: 2015-03-11
• DOI: 10.1093/bioinformatics/btv149
• EISSN: 1367-4811
• ISSN: 1367-4803
• Pmid: 25788627
• Language: English
• Keywords: SBTMR