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Cell Systems Biology


Modeling & Simulation

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SigTran: Hoffman et. al. (Science 2002)

The reaction dynamics of the IkB NF-kb, published by Hoffmann et. al. Science, (2002) has been modeled both deterministically (using JSIM) and stochastically (using SigTran).
The NFkB ODE version of the model in JSIM can be downloaded here. To run the JSIM model one needs to download the software JSIM which is free and available at http://www.physiome.org/.
The stochastic model is done in the software SigTran. This is free and can be downloaded at /teams/modeling/projects/sigtran/index.html. The stochastic version of the model has two stages:
Stage 1: This is the steady state analysis of the model, when there is no activation from the kinase IKK = 0. The steady state simulation is run to get the initial concentrations of different signaling components after long time. This model can be downloaded here.
Stage 2: The model represents the reaction dynamics of Ikb, NFkb reactions when stimulated with IKK = 0.1 uM. In Hoffmann et. al. model, the kinetic rates of the reaction of export of IkBβ mRNA transcripts is a function of time. The present version of SigTran compiler (with GUI) does not support the capability of kinetic rates as functions of time. However, we have modified the compiler specifically for Hoffmann et. al. model with reaction rates of export of IkBβ mRNA transcripts as function of time. The compiler and all the files required to run the model can be downloaded as zipped file here.

NOTE: please read the “ReadMe.txt” file before starting the simulation. The “ReadMe.txt” file contains description of each of the files in the folder and how to run the simulation.

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Department to Bioengineering University of Washington