mcellRules

Overview

Note: This repo is deprecated. Please use the nfsim_dynamic_meshes_pymcell branch instead.

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 the build folder (mcellRules/build), run python requirements.py. This will clone and build:
  • bionetgen
  • nfsim
  • nfsimCInterface
  • MCell
• Create a file named mcellr.yaml in the mcellRules directory (or copy the file mcellr.yaml.template to mcellr.yaml). These are the default paths in that file after running requirements.py:
  • bionetgen: './build/bionetgen/bng2/BNG2.pl'
  • libpath: './build/mcell/lib/'
  • mcell: './build/mcell/build/mcell'

Testing

• The mcellRules/fceri_files directory should initially contain 2 files:

  • fceri.mdlr
  • fceri_ji_comp.geometry.mdl

• From the mcellRules directory, 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
  • fceri_mdl.reactions.mdl
  • fceri_mdl.output.mdl
  • fceri_mdl.molecules.mdl
  • fceri_mdl.main.mdl
  • fceri_mdl.mod_surf_reg.mdl
  • fceri_mdl.surface_classes.mdl
  • fceri.mdlr_extended.xml
  • fceri.mdlr.bngl

• Now use the following command to run mcell with the newly created files: ./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 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,l~Y~pY,a~Y~pY) 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).