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This is an online resource for the paper "Multi-scale model of Mycobacterium tuberculosis infection maps metabolite and gene perturbations to granuloma sterilization predictions."

GranSim-CBM is a multi-scale model combining a constraint-based metabolic model of Mycobacterium tuberculosis with an agent-based model of bacterial growth and host immunity within TB granulomas.

To run GranSim-CBM using the resources below you will need Ubuntu 10.04 or 12.04. If these systems are not available to you, may use Virtualbox.

If you are not using Virtualbox, you may download the model resource archive file from here and unzip the files.

Resources include:
*GranSim-CBM
oInstructions to run the model (README.txt)
oGranSim-CBM executable
- GranSim-CBM executable (grviz-lung)
- Parameter file (BaselineParameterFile.xml)
- Lookup table (Lookup.txt.gz)
- Script to run GranSim-CBM (run-gransim)
- Several Libraries
*CBM
oInstructions to generate a lookup table (README.txt)
oMatlab scripts to generate lookup tables for virtual knockout and wildtype simulations.


To run the models, follow instructions in the README files.

For more information regarding each individual type of model we use GranSim in (multi-scale, multi-compartment, molecular details, etc) please see our individual publications on those topics at: http://malthus.micro.med.umich.edu/lab/tb.html

GranSim Homepage



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