The Design Space Toolbox V2 is a library for analysis of mechanistic models of biochemical systems. This library automates the difficult steps within the System Design Space Approach by combining symbolic and numerical methods for the analysis of systems composed of ordinary differential equations.
The library includes a computer algebra system for parsing and evaluating mathematical expressions and numerical methods for the analysis and visualization of model behaviors. Examples of the Design Space Toolbox V2 through the Python are available at the projects website here.
The preferred installation process is using the Design Space Toolbox V2 update and installation script (see https://bitbucket.org/jglomnitz/toolbox-update-script for detailed instructions). This script manages the Git repositories associated with the C Library, Python Interface, as well as a modified version of the GNU Linear Programming Kit (GLPK) library used by the Design Space Toolbox Project.
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Savageau MA, Coelho PMBM, Fasani RA, Tolla DA, and Salvador A (2009) Phenotypes and tolerances in the design space of biochemical systems. Proc. Natl. Acad. Sci. U.S.A. 106, 6435–6440.
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Savageau MA, and Lomnitz JG (2013) Deconstructing Complex Nonlinear Models in System Design Space, in Discrete and Topological Models in Molecular Biology (Jonoska, N., and Saito, M., Eds.). Springer.
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Fasani RA, and Savageau MA (2010) Automated construction and analysis of the design space for biochemical systems. Bioinformatics 26:2601–2609.
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Lomnitz JG, and Savageau, MA (2013) Phenotypic deconstruction of gene circuitry. Chaos 23, 025108.
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Lomnitz JG, and Savageau MA (2014) Strategy Revealing Phenotypic Differences among Synthetic Oscillator Designs. ACS Synth Biol 3(9):686–701.
Copyright (C) 2010-2015 Jason G. Lomnitz, Department of Biomedical Engineering, University of California, Davis, California, United States. All rights reserved. E-mail: jlomn@ucdavis.edu.
This is part of the Design Space Toolbox V2 project, a software implementation of the System Design Space method developed by Jason G. Lomnitz, originally developed in the laboratory of Michael A. Savageau (for examples of this methodology, see [1-6]). This method decomposes complex nonlinear systems into a finite number of tractable nonlinear subsystems.
The Design Space Toolbox V2 C Library is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.