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A scenario-based approach to modeling development: A prototype model of C. elegans vulval fate specification

Kam N, Kugler H, Marelly R, Appleby L, Fisher J, A. Pnueli, D. Harel, M.J. Stern, and E.J.A. Hubbard

Abstract

Studies of developmental biology are often facilitated by diagram “models” that summarize the current understanding of underlying mechanisms. The increasing complexity of our understanding of development necessitates computational models that can extend these representations to include their dynamic behavior. Here we present a prototype model of Caenorhabditis elegans vulval precursor cell fate specification that represents many processes crucial for this developmental event but that are hard to integrate using other modeling methodologies. We demonstrate the integrative capabilities of our methodology by comprehensively incorporating the contents of three seminal papers, showing that this methodology can lead to comprehensive models of developmental biology. The prototype computational model was built and is run using a language (Live Sequence Charts) and tool (the Play-Engine) that facilitate the same conceptual processes biologists use to construct and probe diagram-type models. We demonstrate that this modeling approach permits rigorous tests of mutual consistency between experimental data and mechanistic hypotheses and can identify specific conflicting results, providing a useful approach to probe developmental systems.

Details

Publication typeArticle
Published inDevelopmental Biology
URLhttp://dx.doi.org/doi:10.1016/j.ydbio.2008.07.030
Pages1-5
Volume323
Number1
PublisherElsevier
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