Bionet is intended to provide a computational tool for modeling biological pathways or biosystem dynamics on multiple scales. At this time, manual descriptions of gene and protein interactions are described in text files with a simple format.The methodology in bionet is distinguished from previous qualitative modeling approaches in several ways. The goal was to develop a model that would allow experimental biologists to use the kind of qualitative data found in typical journal articles to describe the interaction of genes, proteins, and other cellular components to create computer models of large numbers of interacting parts. This arose from a practical need in our research to keep track of myriad components in pathway models that were built from data extracted from dozens of journal articles. Biologists already do this kind of mental modeling every time they make a new hypothesis; a tool was needed to aid in this reasoning. Secondly, with new sources of data becoming available, it was important to design a methodology that could be expanded in the future to integrate new data sources to refine models.
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Bosl, W. J. (2007).
Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery.
BMC Syst Biol, 1, 13.