MONOD, a Collaborative Tool for Manipulating Biological Knowledge
Name
Monod-Soergel-Oct2004.pdf
Size
1.87 MB
Format
Adobe PDF
Checksum (MD5)
35ead5b885fad97f7a40d640e9d4b853
Author(s)
Soergel, David
Choi, Kirindi
Thomson, Ty
Doane, Jay
George, Brian
Morgan-Linial, Ross
Brent, Roger
Endy, Drew
Date Issued
June 19, 2008
Abstract
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.
Description
Research article written in 2004 describing MONOD, an early biological knowledge management system
Subjects
biology
knowledge management
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
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