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Wolfram Research Mathematica

Mathematica is a general computer software system and language intended for mathematical and other applications. You can use Mathematica as: A numerical and symbolic calculator where you type in questions, and Mathematica prints out answers, a visualization system for functions and data, a high-level programming language in which you can create programs, large and small ones. and a modeling and data analysis environment.

Rule-Based Modeling of Biochemical Systems with BioNetGen

Rule-based modeling involves the representation of molecules as structured objects and molecular interactions as rules for transforming the attributes of these objects.  The approach is notable in that it allows one to systematically incorporate site-specific details about protein-protein interactions into a model. BioNetGen allows a user to create a computational model that characterizes the dynamics of a signal transduction system, and that accounts comprehensively and precisely for specified enzymatic activities, potential post-translational modifications and interactions of the domains of signaling molecules. The output defines and parameterizes the network of molecular species that can arise during signaling and provides functions that relate model variables to experimental readouts of interest. Models that can be generated are relevant for rational drug discovery, analysis of proteomic data and mechanistic studies of signal transduction.

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