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Rule Based Modelling in Space - the SRSim Simulator

biosys
biosys
biosys

These Pictures were generated using SRSim and Visual Molecular Dynamics (VMD).

Features in Development:

  • allow state and modification changes to be observed from the outside
  • allow wildcards for exchange rules
  • allow more than a single modification to be executed for one modification rule


Manual: in short - here

Main Paper: see doi:10.1186/1471-2105-11-307
Tutorial: see doi:10.1007/978-3-642-18123-8_19

current version 2.08

old version 2.05

  • some more bug-fixes, see RuleSys/defs.h for details
  • added a plot feature, so that the graph structure of all the molecules in the reactor can be written to a file.

download:


old version 2.04

  • some bug-fixes, see RuleSys/defs.h for details

download:


old version 2.02

  • allows the addition and deletion of molecules through reaction rules (full support of exchange rules)

download:


old version 2.01

new features:

  • Dihedral Angles can now be defined for a simulation
  • General framework to define global simulation parameters as force terms and tolerances - those had to be defined at different positions in the
     

download:


old versions: 1.00

  • was published together with the BMC Bioinformatics article.
  • update to the example sources, that were supplied with the BMC Bioinformatics article (typos that made the simulator crash).