STOCHSIM

STOCHSIM: modelling of stochastic biomolecular processes. Summary: StochSim is a stochastic simulator for chemical reactions. Molecules are represented as individual software objects that react according to probabilities derived from concentrations and rate constants. Version 1.2 of StochSim provides a novel cross-platform graphical interface written in Perl/Tk. A simple two-dimensional spatial structure has also been implemented, in which nearest-neighbour interactions of molecules in a 2-D lattice can be simulated. Availability: Various ports of the program can be retrieved at ftp://ftp.cds.caltech.edu/pub/dbray/

Keywords for this software

Anything in here will be replaced on browsers that support the canvas element

References in zbMATH (referenced in 6 articles )

Showing results 1 to 6 of 6.
Sorted by year (citations)

  1. Suderman, Ryan; Mitra, Eshan D.; Lin, Yen Ting; Erickson, Keesha E.; Feng, Song; Hlavacek, William S.: Generalizing Gillespie’s direct method to enable network-free simulations (2019)
  2. J. M. G. Vilar, L. Saiz: CplexA: a Mathematica package to study macromolecular-assembly control of gene expression (2010) arXiv
  3. Tindall, M. J.; Porter, S. L.; Maini, P. K.; Gaglia, G.; Armitage, J. P.: Overview of mathematical approaches used to model bacterial chemotaxis. I: The single cell (2008)
  4. Miller, David J.; Ghosh, Avijit: A fully adaptive reaction-diffusion integration scheme with applications to systems biology (2007)
  5. Manninen, Tiina; Linne, Marja-Leena; Ruohonen, Keijo: Developing Itô stochastic differential equation models for neuronal signal transduction pathways (2006)
  6. Weitzke, Elizabeth L.; Ortoleva, Peter J.: Simulating cellular dynamics through a coupled transcription, translation, metabolic model. (2003)