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Table of Contents

Design Space Toolbox Preliminaries

1. Technology Overview.
2. Installing the Design Space Toolbox V2.
3. The IPython notebook widget interface.

Formulating a problem using the Design Space Toolbox

1. Design space preliminaries: model formulation and recasting.
2. Toolbox input: model equations and architectural constraints.
3. Creating a system design space object.

Enumerating the Phenotypic Repertoire

1. IPython Notebook Preamble.
2. Enumerating the phenotypic repertoire, and its subsets.
3. Qualitatively distinct phenotypes and their dominant S-system.
4. Global-perspective of the repertoire of phenotypic characteristics.

Determining parameter values for Cases

1. IPython Notebook Preamble.
2. Automatically determined values for the parameters.
3. Local analyses about the automatically determined values for the parameters.
4. Automatically determined 'biological' values for the parameters.

Simultaneous realization of multiple phenotypes.

1. IPython Notebook Preamble.
2. Co-localizing cases in a 1-D slice.
3. Co-localizing cases in 2-D and \(n\)-D slices.
4. Arranging cases for a specific behavior.

References

Supporting Materials

Toy Models

1. Toy Model 1.
2. Toy Model 2.

Suggested Papers

1. Design space method

2. Automated method for elucidating genotype–phenotype map [Paper has been assigned a DOI, but has not been published as of 9/4/15.]
   
   

3. Comparison of Synthetic Oscillators

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Jason G. Lomnitz
Savageau Lab
Department of Biomedical Engineering
University of California
Davis, CA 95616
jlomn@ucdavis.edu