
The BioNetGen source code 'MAPK.bngl' accompanies the article:

   "Relaxation oscillations and hierarchy of feedbacks in MAPK signaling"

       by  Kochanczyk M, Kocieniewski P, Kozlowska E, Jaruszewicz J, 
             Sparta B, Pargett M, Albeck JG, Hlavacek WS, 
                             and Lipniacki T

                        (Scientific Reports, 2016)

and allows for both deterministic (ODEs) and stochastic (Gillespie direct SSA)
simulation.

For a description of the BioNetGen language (BNGL), see e.g.:

 * Faeder JR, Blinov ML, Hlavacek WS"
  "Rule-based modeling of biochemical systems with BioNetGen". 
   Methods Mol. Biol. 500, 113-167 (2009).

The 'export' folder contains an executable Matlab script and SBML model 
definition, which are equivalent to the model specified in BNG in MAPK.bngl,
and were exported by BioNetGen using the BNGL file.


Model execution instructions
----------------------------

The most convenient way to execute the model is to download RuleBender from
http://www.rulebender.org, install it (following its installation instructions),
and paste the contents of the MAPK.bngl file into an empty BNGL file created 
in a new RuleBender project. If this solution is not working, alternatively,
you can:

1) Download BioNetGen from http://www.bionetgen.org and install the 
software following the step-by-step instructions provided in the tutorial.
(This may require the installation of Perl and, optionally, Java.)

2) Place the file 'MAPK.bngl' into the folder 'Models2' in the BioNetGen 
directory.

3) In the command window under Windows: change the current working directory 
to 'Models2' in your installed BioNetGen directory by issuing e.g.

  cd "C:\Program Files\BioNetGen-2.2.6-stable\Models2"

and then run BioNetGen engine with the following command:

  perl ..\BNG2.pl MAPK.bngl

(Proceed analogously under Linux/Mac OS X.)


Output will be written in files: MAPK_Fig4A.gdat, MAPK_Fig4B.gdat, 
MAPK_Fig4C.gdat in the Models2 directory. 

In case you do not use RuleBender, you can visualize individual trajectories
using e.g. PhiBPlot, which is contained in the BioNetGen installation directory 
(Java required). Under Windows, double-click the application jar file and select
GDAT-file; under under Linux/Mac OS X type in the command line:

  java -jar YOUR_BIONETGEN_DIR/PhiBPlot/PhiBPlot.jar PATH_TO_A_GDAT_FILE


-- Wed Apr 15 13:19:50 MDT 2015

