Functional modelling of biochemical networks

NetBuilder and BioTapistry are interactive tools for building, visualizing, and simulating the behaviour of biochemical networks, specifically genetic regulatory networks (GRNs). GRNs perform the lowest level coarse regulation in processes such as cell differentiation and response to external signals. Both tools depict the networks using the functional model notation (data flow diagrams), and the resulting graphs are reminiscent of electronic circuit diagrams: data (molecules) are channelled via arcs between nodes that carry out certain transformations (chemical and physical processes). The notation used by NetBuilder and BioTapstry is different from the dynamic model notation (state transition diagrams) that is commonly used to represent chemical reaction networks, and is, it is hoped, more amenable to composite modelling and simulation. I will describe the structure, use, and potential of these tools, and I will also discuss two related international efforts to develop a standard XML-based language for describing biochemical networks (Systems Biology Markup Language, SBML, and the Cell Markup Language, CellML).


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