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- Nicholas A. Allen, Laurence Calzone, +8 authors Jason W. Zwolak
- Omics : a journal of integrative biology
- 2003

The life of a cell is governed by the physicochemical properties of a complex network of interacting macromolecules (primarily genes and proteins). Hence, a full scientific understanding of and rational engineering approach to cell physiology require accurate mathematical models of the spatial and temporal dynamics of these macromolecular assemblies,… (More)

- Marc Vass, Nicholas A. Allen, Clifford A. Shaffer, Naren Ramakrishnan, Layne T. Watson, John J. Tyson
- Bioinformatics
- 2004

SUMMARY
We describe the JigCell Model Builder (JCMB), a tool for creating biochemical reaction network models. JCMB is designed for ease of use and its interface uses the standard spreadsheet metaphor. The JigCell Run Manager (JCRM) is a tool for organizing the large collections of simulation runs typically required by reaction network modeling activities.… (More)

- Nicholas A. Allen, Clifford A. Shaffer, Layne T. Watson
- Proceedings of the Winter Simulation Conference…
- 2005

Successfully building a model requires a combination of expertise in the problem domain and in the practice of modeling and simulation (M&S). Model verification, validation, and testing (VV&T) are essential to the consistent production of models that are useful and correct. There are significant communities of domain experts that build and use models… (More)

Successfully building a model requires a combination of expertise in the problem domain and in the practice of modeling and simulation (M&S). Model verification, validation, and testing (VV&T) are essential to the consistent production of models that are useful and correct. There are significant communities of domain experts that build and use models… (More)

- Nicholas A. Allen, Clifford A. Shaffer, Naren Ramakrishnan, Marc T. Vass, Layne T. Watson
- Simulation
- 2003

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… (More)

- Thomas D. Panning, Layne T. Watson, Nicholas A. Allen, Katherine C. Chen, Clifford A. Shaffer, John J. Tyson
- J. Global Optimization
- 2008

Two parallel deterministic direct search algorithms are used to find improved parameters for a system of differential equations designed to simulate the cell cycle of budding yeast. Comparing the model simulation results to experimental data is difficult because most of the experimental data is qualitative rather than quantitative. An algorithm to convert… (More)

- Nicholas A. Allen, Katherine C. Chen, Clifford A. Shaffer, John J. Tyson, L. T. Watson
- Systems biology
- 2006

Cellular processes are governed by complex networks of interacting genes and proteins. Theoretical molecular biologists attempt to describe these processes via mathematical models by writing biochemical reaction equations. Modellers are building increasingly larger and complex mathematical models to describe these cellular processes, making model evaluation… (More)

Two parallel deterministic direct search algorithms are used to find improved parameters for a biological model. The model is a system of differential equations designed to simulate the cell cycle of budding yeast. Comparing the model simulation results to experimental data is difficult because most of the experimental data is qualitative rather than… (More)

The cell is a highly ordered and intricate machine within which a wide variety of chemical processes take place. The full scientific understanding of cellular physiology requires accurate mathematical models that depict the temporal dynamics of these chemical processes. Modelers build mathematical models of chemical processes primarily from systems of… (More)

- Nicholas A. Allen, Clifford A. Shaffer, Marc Vass, Naren Ramakrishnan, Layne T. Watson
- Winter Simulation Conference
- 2003

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… (More)

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