Open Access Research article

The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail

Katrin Kolczyk*, Regina Samaga, Holger Conzelmann, Sebastian Mirschel and Carsten Conradi

Author Affiliations

Max Planck Institute Magdeburg, 39106 Magdeburg, Sandtorstr. 1, Germany

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BMC Bioinformatics 2012, 13:251  doi:10.1186/1471-2105-13-251

Published: 28 September 2012

Additional files

Additional file 1:

Process-Interaction-Model of EGF insulin crosstalk (additional information). Additional file 1 lists the reaction rules and the associated parameters taken from [7] and used to elaborate the EGF insulin crosstalk example in the section “Results”. The process nodes of the PIM are correlated to the reaction rules in a tabular fashion. Furthermore, all parameter tables associated to the process nodes of the PIM are given.

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Additional file 2:

Input file for the software BioNetGen (EGF insulin crosstalk). Additional file 2 contains the rule-based model obtained from the PIM describing EGF insulin crosstalk (section Results) and can be used as an input file for BioNetGen.

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Open Data

Additional file 3:

Input files for the softwareCellNetAnalyzer (EGF insulin crosstalk). This archive contains all files of the logical model obtained from the PIM describing EGF insulin crosstalk (section Results) in CellNetAnalyzer format. CellNetAnalyzer is available from http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html webcite.

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