There's more to a model than code: understanding and formalizing in silico modeling experience

Wiles, Janet, Geard, Nicholas L., Watson, James, Willadsen, Kai, Mattick, John, Bradley, Daniel and Hallinan, Jennifer (2005). There's more to a model than code: understanding and formalizing in silico modeling experience. In: Proceedings of the 2005 Workshops on Genetic and Evolutionary Computation. GECCO'05: The Genetic and Evolutionary Computation Conference 2005, Washington, DC, USA, (281-288). 25-29 June, 2005. doi:10.1145/1102256.1102318


Author Wiles, Janet
Geard, Nicholas L.
Watson, James
Willadsen, Kai
Mattick, John
Bradley, Daniel
Hallinan, Jennifer
Title of paper There's more to a model than code: understanding and formalizing in silico modeling experience
Conference name GECCO'05: The Genetic and Evolutionary Computation Conference 2005
Conference location Washington, DC, USA
Conference dates 25-29 June, 2005
Proceedings title Proceedings of the 2005 Workshops on Genetic and Evolutionary Computation
Journal name ACM Digital Library
Place of Publication New York, NY, USA
Publisher Association for Computing Machinery
Publication Year 2005
Sub-type Fully published paper
DOI 10.1145/1102256.1102318
Open Access Status
Start page 281
End page 288
Total pages 8
Language eng
Formatted Abstract/Summary
Mapping biology into computation has both a domain specific aspect -- biological theory -- and a methodological aspect -- model development. Computational modelers have implicit knowledge that guides modeling in many ways but this knowledge is rarely communicated. We review the challenge of biological complexity and current practices in modeling genetic regulatory networks with the aim of understanding characteristics of the in silico modeling process and proposing directions for future improvements. Specifically, we contend that the modeling of complex biological systems can be made more efficient and more effective by the use of structured methodologies incorporating experience about modeling algorithms and implementation. We suggest that an appropriate formalism is Complex Systems Patterns, adopted from Design Patterns in software engineering. First steps towards building community resources for such patterns are described.
Q-Index Code E1
Q-Index Status Provisional Code
Institutional Status UQ

 
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Created: Tue, 10 Mar 2015, 12:23:16 EST by James Watson on behalf of School of Information Technol and Elec Engineering