6533b881fe1ef96bd12d7d0c

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Additional file 1 of Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters – the case of phage λ

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Software package implementing our proposed method of attractor analysis. It contains source files, user manual and the phage λ model described in this manuscript. Following subsections describe files from the package. ModelDescription.txt: Definition of the phage λ model that is analysed within this paper. ModelConstraints.txt: File that specifies partial constraints for the orderings of binding site affinities. Here, the constraints are applicable to our phage λ model. HSM_graph_analysis.cpp: The main component of the software that identifies all feasible states of a system. HSM_graph_analysis.h: The second component of the software for graph analysis. It is a C++ header file which contains definitions of classes and data structures. HSM_instructions.pdf: Instructions for compiling and running the software that constructs a graph describing all possible states of a system. Formats of input and output files are described as well. Thr.txt: File containing the orderings of binding site affinities for all proteins. ExtractStates.pl: Perl script that extracts all stable states from a state transition graph. MergeStates.pl: Perl script that characterises and summarises stable states. It aggregates the information about stable states for several state graphs. AnalyseStates.pl: Perl script that characterises stable states of a system by describing the feasible behaviours within them. ThresholdOrderings.pl: Perl script that generates all linear orderings of binding site thresholds that are consistent with a set of constraints defining partially known orderings. (ZIP 84 kb)