

=== About ===
This is a simple model of E.coli heat shock. It was developed to demonstrate
how to integrate stochastic (Gillespie) and deterministic (ODE) sub-models
using ECELL 3.   Computational procedures for the main model and the
protein folding sub-model can be specified separately.   

=== Files and directories ===

README:         This file
heatshock.em    Model file (em file) for this model.

=== Running this model ===
1. (If necessary) Convert the .em file to .eml file.

   % ecell3-em2eml heatshock.em
   % ls heatshock.eml
   heatshock.eml

2. Run gecell, File->loadModel and load the heatshock.eml file.

=== Configure this model ===

In the begining of heatshock.em file:


        @#{MAIN_STEPPER='DE1'}
        @#{MAIN_PROCESS='MassActionFluxProcess'}
        @{HYBRID_STEPPER='DE1'}
        @{HYBRID_PROCESS='MassActionFluxProcess'}

        @{MAIN_STEPPER='NR1'}
        @{MAIN_PROCESS='GillespieProcess'}
        @#{HYBRID_STEPPER='NR1'}
        @#{HYBRID_PROCESS='GillespieProcess'}

Is the config for the model. In current setting, Hybrid part will be run using
MassActionFluxProcess where the reactions basedon MAIN_STEPPER will call 
GillespieProcess.

To run a purely stochastic model:

        @#{MAIN_STEPPER='DE1'}
        @#{MAIN_PROCESS='MassActionFluxProcess'}
        @#{HYBRID_STEPPER='DE1'}
        @#{HYBRID_PROCESS='MassActionFluxProcess'}

        @{MAIN_STEPPER='NR1'}
        @{MAIN_PROCESS='GillespieProcess'}
        @{HYBRID_STEPPER='NR1'}
        @{HYBRID_PROCESS='GillespieProcess'}

To run a purely deterministic model:
        @{MAIN_STEPPER='DE1'}
        @{MAIN_PROCESS='MassActionFluxProcess'}
        @{HYBRID_STEPPER='DE1'}
        @{HYBRID_PROCESS='MassActionFluxProcess'}

        @#{MAIN_STEPPER='NR1'}
        @#{MAIN_PROCESS='GillespieProcess'}
        @#{HYBRID_STEPPER='NR1'}
        @#{HYBRID_PROCESS='GillespieProcess'}
