Research article written in 2004 describing MONOD, an early biological knowledge management systemWe 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
