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Open Access Research article

Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles

John Jack, John F Wambaugh and Imran Shah*

Author Affiliations

National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA

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BMC Systems Biology 2011, 5:109  doi:10.1186/1752-0509-5-109

Published: 11 July 2011

Additional files

Additional file 1:

Evaluation of Network Behavior for Protein Knockouts. The heatmap shows the simulation results for deleting individual proteins from the network. Each cell in the heatmap represents the mean protein activity at steady state relative to control across 20 replicates with 100 cells per replicate. The color intensity indicates the protein (x-axis) behavior at steady state relative to the baseline simulation (no protein knockout). The y-axis indicates the protein deletion.

Format: DOC Size: 125KB Download file

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Additional file 2:

network_model.zip. The Cytoscape export files for the crosstalk network model on AP-1 formation. These files are to be used in conjunction with the python_simulation_code.

Format: ZIP Size: 2KB Download file

Open Data

Additional file 3:

python_simulation_code.zip. The source code to load the network model and produce the simulation results reported in the paper. Refer to the README file for instruction.

Format: ZIP Size: 16KB Download file

Open Data