MONOD, a Collaborative Tool for Manipulating Biological Knowledge
Author(s)Soergel, David; Choi, Kirindi; Thomson, Ty; Doane, Jay; George, Brian; Morgan-Linial, Ross; Brent, Roger; Endy, Drew; ... Show more Show less
We describe an open source software tool called MONOD, for Modeler’s Notebook and Datastore, designed to capture and communicate knowledge generated during the process of building models of many-component biological systems. We used MONOD to construct a model of the pheromone response signaling pathway of Saccharomyces cerevisiae. MONOD allowed the accumulation, documentation, and exchange of data, valuations, assumptions, and decisions generated during the model building process. MONOD thus helped preserve a record of the steps taken on the path between from the experimental data to the computable model. We believe that MONOD and its successors may streamline the processes of building models, communicating with other researchers, and managing and manipulating biological knowledge. "Collaborative annotation"-- fine-grained, structured, searchable communication enabled by software tools of this type-- could positively affect the practice of biological research.
Research article written in 2004 describing MONOD, an early biological knowledge management system
biology, knowledge management
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