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

Na'aman Kam; Hillel Kugler; Rami Marelly; Lara Appleby; Jasmin Fisher; Amir Pnueli; David Harel; Michael J. Stern; E. Jane Albert Hubbard

doi:10.1016/j.ydbio.2008.07.030

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

Na'aman Kam, Hillel Kugler, Rami Marelly, Lara Appleby, Jasmin Fisher, Amir Pnueli, David Harel, Michael J. Stern, E. Jane Albert Hubbard

Research output: Contribution to journal › Article › peer-review

32 Scopus citations

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.

Original language	English
Pages (from-to)	1-5
Number of pages	5
Journal	Developmental Biology
Volume	323
Issue number	1
DOIs	https://doi.org/10.1016/j.ydbio.2008.07.030
State	Published - 1 Nov 2008
Externally published	Yes

Bibliographical note

Funding Information:
We gratefully acknowledge the contributions of D. Barak, and M. Yano to various aspects of this work. In addition, we thank R. Posner, L. Cooley, and K. Birnbaum for critical reading of early versions of the manuscript. This work was supported by collaborative NIH grant R24-GM066969, the Yale-Weizmann Exchange Program, and the John von Neumann Minerva Center at the Weizmann Institute of Science. Appendix A

Funding

We gratefully acknowledge the contributions of D. Barak, and M. Yano to various aspects of this work. In addition, we thank R. Posner, L. Cooley, and K. Birnbaum for critical reading of early versions of the manuscript. This work was supported by collaborative NIH grant R24-GM066969, the Yale-Weizmann Exchange Program, and the John von Neumann Minerva Center at the Weizmann Institute of Science. Appendix A

Funders	Funder number
National Institutes of Health
National Institute of General Medical Sciences	R24GM066969
Weizmann Institute of Science

Keywords

C. elegans
Live Sequence Charts
Modeling
Scenario-based
VPC
Vulval fate specification

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10.1016/j.ydbio.2008.07.030

Cite this

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

Abstract

Bibliographical note

Funding

Keywords

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