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Improving the Development Process for Eukaryotic Cell Cycle Models with a Modeling Support Environment

Nicholas A. Allen

Department of Computer Science, Virginia Polytechnic Institute and State University Blacksburg, VA 24061-0106

Clifford A. Shaffer

Department of Computer Science, Virginia Polytechnic Institute and State University Blacksburg, VA 24061-0106, shaffer{at}vt.edu

Naren Ramakrishnan

Department of Computer Science, Virginia Polytechnic Institute and State University Blacksburg, VA 24061-0106

Marc T. Vass

Department of Computer Science, Virginia Polytechnic Institute and State University Blacksburg, VA 24061-0106

Layne T. Watson

Department of Computer Science, Virginia Polytechnic Institute and State University Blacksburg, VA 24061-0106

Theoretical molecular biologists attempt to describe cellular processes and regulatory networks with continuous and discrete mathematical models. Previous practice has been to develop models largely by hand and then to validate them primarily by comparing time-series plots versus the observed experimental results. The authors report their experiences in designing and building a modeling support environment for cell cycle models. They describe improvements to the development process for molecular network models by (a) identifying the key elements of the existing modeling process, (b) incorporating simulation methodology into a revised modeling process, and (c) building and testing software that supports the revised modeling process.

Key Words: Support environment • systems biology • hybrid systems • regulatory networks

SIMULATION, Vol. 79, No. 12, 674-688 (2003)
DOI: 10.1177/0037549703040944
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