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Most biological processes are controlled by regulatory networks, which involve various kinds of molecular interactions, including protein-mediated transcriptional regulations, polypeptide receptor–ligand associations, protein modifications by specific enzymes, etc. Decades of genetic and molecular analyses, more recently complemented by high-throughput functional genomic experiments, have progressively uncovered many of the numerous interactions controlling several crucial biological processes (including cell cycle and various developmental pathways). The complexity of the networks delineated often defies intuitive reasoning, consequently calling for the development of proper computational tools. Different mathematical approaches have been proposed to model such genetic networks and to simulate their dynamical behaviour, ranging from quantitative formalisms to crude Boolean models.
(Gonzalez et al, 2006) GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. Biosystems.