Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters – the case of phage λ
Background Gene regulatory networks can be modelled in various ways depending on the level of detail required and biological questions addressed. One of the earliest formalisms used for modeling is a Boolean network, although these models cannot describe most temporal aspects of a biological system. Differential equation models have also been used to model gene regulatory networks, but these frameworks tend to be too detailed for large models and many quantitative parameters might not be deducible in practice. Hybrid models bridge the gap between these two model classes – these are useful when concentration changes are important while the information about precise concentrations and binding…
Additional file 1 of Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters – the case of phage λ
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 contain…