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mcellRules

Overview

MCellR lets you leverage the power of bionetgen's rule based modeling within the reaction-diffusion simulator MCell.

Using mdlr2mdl.py, you can convert MDLR files into MDL files. MDLR is similar to MDL except it has bionetgen-style syntax for portions of the molecule definitions, reactions, releases, and reaction data. After creating the MDL files using mdlr2mdl.py, the simulation should be run using a special feature branch of MCell (nfsim_diffusion). As the simulation runs, MCell will call the NFsim library as needed in order to find reaction partners.

Installation

  • In build folder, run python requirements.py. This file will download and compile, bionetgen, nfsim, nfsimCinterface, and MCell. (May need troubleshooting)
  • Create a file called mcellr.yaml in the mcellRules directory.
    • Set the path to bionetgen, which should be ./mcellRules/build/bionetgen/bng2/BNG2.pl.
    • Set the "libpath" which should be in ./mcellRules/build/mcell/lib if you ran requirements.py.
    • Look at mcellr.yaml.template for a reference.

Testing

  • Run the following command: python mdlr2mdl.py -ni ./fceri_files/fceri.mdlr -o ./fceri_files/fceri_mdl (use Python 2, not 3, for this part).
  • This will create the following files within the fceri_files directory:
    • fceri.mdlr.xml
    • fceri.mdlr_total.xml
    • fceri_mdl.seed.mdl
    • tfceri_mdl.reactions.mdl
    • fceri_mdl.output.mdl
    • fceri_mdl.molecules.mdl
    • fceri_mdl.main.mdl
  • Now use the following command to run newly created mdl file: ./build/mcell/build/mcell ./fceri_files/fceri_mdl.main.mdl -n ./fceri_files/fceri.mdlr_total.xml
  • This will create the following output files in the main mcellRules directory:
    • fceri.mdlr_total.xml.gdat
    • fceri.mdlr_total.xml_reactions.gdat

Syntax

For a general overview of MDL, please see the quick reference guide.

MDLR is an extension of MDL using bionetgen style syntax. All of the MDL blocks (e.g. DEFINE_MOLECULE, DEFINE_REACTIONS, etc) are prefaced with a pound sign like this:

#DEFINE_MOLECULES {
  ..
}

#DEFINE_REACTIONS {
  ..
}

Molecules

For molecules, the names are treated like bionetgen molecules like Syk(tSH2,lYpY,aYpY) in the following example:

#DEFINE_MOLECULES
{
  Syk(tSH2,l~Y~pY,a~Y~pY)
  {
      DIFFUSION_CONSTANT_3D = 8.51e-7 
  }
}

This example shows a molecule named Syk with three different components (tSH2, l, and a). Two of the components (l and a) each have two different states (Y and pY).