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MATLAB code for Metabolic Economics

Metabolic economics is a theory optimal metabolic behaviour in cells. Complementing existing approaches for modelling cell metabolism, it employs a notion of "economic value" to characterize the importance of individual metablites, fluxes, and enzyme (for example, their impact on the achievable rate of biomass production).

This repository contains Matlab functions to compute and analyse metabolic values, extending the Metabolic Network Toolbox.

Dependencies

o Matlab utility functions (https://github.com/liebermeister/matlab-utils)

o Metabolic Network Toolbox (https://github.com/liebermeister/metabolic-network-toolbox)

o SBMLtoolbox ( http://sbml.org/Software/SBMLToolbox)

o SBtab toolbox (https://github.com/liebermeister/sbtab-matlab)

o efmtool ( http://www.csb.ethz.ch/tools/efmtool)

Please make sure that these matlab packages are installed in your system and that all these directories and subdirectories are included in your matlab path.

Installation

Please see the installation instructions.

License

This package is released under the GNU General Public License.

Contact

Please contact Wolfram Liebermeister with any questions or comments.

References

Liebermeister W. (2018), Optimal metabolic states in cells, biorXiv doi:10.1101/483867

Liebermeister W. (2018), The value structure of metabolic states, biorXiv doi:10.1101/483891

Liebermeister W. (2014), Enzyme economy in metabolic networks, arXiv:1404.5252

Liebermeister W. (2014), How enzyme economy shapes metabolic fluxes, arXiv:1404.5072

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