https://github.com/princetonuniversity/flux-ratio-based-gibbs-energy
Determine free energy of reaction and its confidence interval via metabolic flux analysis and optimization
https://github.com/princetonuniversity/flux-ratio-based-gibbs-energy
Last synced: 7 months ago
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Determine free energy of reaction and its confidence interval via metabolic flux analysis and optimization
- Host: GitHub
- URL: https://github.com/princetonuniversity/flux-ratio-based-gibbs-energy
- Owner: PrincetonUniversity
- License: mit
- Created: 2015-07-28T01:44:57.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2015-12-18T16:49:01.000Z (almost 10 years ago)
- Last Synced: 2025-01-21T09:30:44.615Z (9 months ago)
- Language: Matlab
- Size: 43.9 MB
- Stars: 8
- Watchers: 17
- Forks: 3
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# flux-ratio-based-gibbs-energy
Determine Gibbs free energy of reaction and its confidence interval via metabolic flux analysis and optimization
Integrate absolute cellular metabolite concentrations with flux-derived Gibbs energies and refine confidence intervals
Code used in:
Metabolite concentrations and free energies that favor efficient enzyme usage are a conserved feature of cellular metabolism
Junyoung O. Park, Sara A. Rubin, Yi-Fan Xu, Daniel Amador-Noguez, Jing Fan, Tomer Shlomi, Joshua D. Rabinowitz
Princeton University
In each organism folder,
- *_mea.xlsx contains measured labeling fractions, measured fluxes, and net/exchange flux inequality constraints that went into the model as input
- .xml shows the metabolites, reactions, carbon mapping, and flux equality constraints
- .h5 and .m function contain the stoichiometric matrix, its kernel, and the cumomer model
- .mat file contains the genome scale model with measured metabolie concentrations and reaction free energies
In brenda folder,
- python script to obtain Km and Ki values from BRENDA
In integrate folder,
- matlab script to solve the quadratic programming (optimal concentration and free energy set) and the linear programming (their refined lower and upper bounds) problems
- output model has two new fields: (1) .metConc shows best fit concentrations in M (col 1) with L.B. (col 2) and U.B. (col 3); (2) .rxndG2 shows best fit Gibbs free energy in kJ/mol (col 1) with L.B. (col 2) and U.B. (col 3)
To run MFA, obtain Gibbs energy of reaction, and integrate metabolite concentrations and Gibbs free energies,
1) Open Matlab 2013b or newer
2) Set Path -> Add Folder -> Choose ./src -> Save
3) Open (*_)script.m and execute
4) To run it parallel, enter 'matlabpool local 4' on the command line. '4' can be a different number if a different number of cores is desired
5) Running on clusters requires an additional setup. Please contact system administrator
6) For the concentration-Gibbs energy integration, run integrate/run_interconfint.m