Algorithm 676: ODRPACK: software for weighted orthogonal distance regression
ACM Transactions on Mathematical Software (TOMS)
Developing user interfaces: ensuring usability through product & process
Developing user interfaces: ensuring usability through product & process
Lipschitzian optimization without the Lipschitz constant
Journal of Optimization Theory and Applications
Covalidation of dissimilarly structured models
Proceedings of the 29th conference on Winter simulation
Verification, validation, and accreditation
Proceedings of the 30th conference on Winter simulation
The methodology roles in the realization of a model development environment
WSC '88 Proceedings of the 20th conference on Winter simulation
Credibility assessment of simulation results
WSC '86 Proceedings of the 18th conference on Winter simulation
Model generation issues in a simulation support environment
WSC' 90 Proceedings of the 22nd conference on Winter simulation
V&A; III: verification and validation without independence: a recipe for failure
Proceedings of the 32nd conference on Winter simulation
Supporting creativity in problem solving environments
C&C '02 Proceedings of the 4th conference on Creativity & cognition
Dynamic Data Structures for a Direct Search Algorithm
Computational Optimization and Applications
Error Detection Support in a Cellular Modeling End-User Programming Environment
HCC '02 Proceedings of the IEEE 2002 Symposia on Human Centric Computing Languages and Environments (HCC'02)
Proceedings of the 34th conference on Winter simulation: exploring new frontiers
The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle
Journal of Global Optimization
KINSOLVER: A simulator for computing large ensembles of biochemical and gene regulatory networks
Computers & Mathematics with Applications
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Biological pathway modelers attempt to describe cellular processes and regulatory networks with continuous and discrete models of the cell cycle. Previous practice has been to develop these models largely by hand, and then to validate models primarily by comparing time series plots versus the observed experimental results. This paper reports our experiences in designing and building a modeling support environment (MSE) for cell cycle models. We describe improvements to the development process for cell cycle models by (a) identifying the key elements of the existing modeling process, (b) applying simulation methodology to construct a revised modeling process, and (c) building and testing software that supports the revised modeling process.