https://github.com/robaina/scirep2017
Supplementary Information
https://github.com/robaina/scirep2017
Last synced: about 1 year ago
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Supplementary Information
- Host: GitHub
- URL: https://github.com/robaina/scirep2017
- Owner: Robaina
- Created: 2017-07-22T08:48:34.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2017-07-22T08:51:03.000Z (almost 9 years ago)
- Last Synced: 2025-04-06T10:38:03.339Z (about 1 year ago)
- Language: Matlab
- Homepage:
- Size: 1.16 MB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# SciRep2017
This folder contains the MATLAB functions and data used to generate all computational results presented in:
"Resolving the central metabolism of Arabidopsis guard cells"
Semidán Robaina-Estévez1*, Danilo de Menezes Daloso2,3*, Youjun Zhang2, Alisdair R. Fernie2, Zoran Nikoloski1**
1Systems Biology and Mathematical Modeling Group, 2Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany, 3Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brasil.
Scientific Reports, 2017
MainFunction contains the code to generate all results and calls the rest of the functions
GEM&DATA contains the Arabidopsis genome-scale model used in this study, the expression data (already preprocessed in R, see details in the publication) and two MATLAB structures: RESULTS and RESULTSCBC. These structures contain the solution generated with the G and M alternative optimal flux distributions sampled on this study when no additional constraints are imposed, and when a constraint on the ratio of carboxylation to oxygenation and reactions 11, 13 and 14 in the CBC are constraint to carry flux.The field "GCMlist" in each of these structures contains a list of all reactions in AraCOREred (split in forward and backward direction), the mean flux values, the p-values of the Mann-Whitney tests and the maximum and minimum flux values calculated with RegrExFVA.
These functions depend on a working installation of Gurobi. Academic licenses can be requested from: http://www.gurobi.com"
Questions can be addressed to: robaina@mpimp-golm.mpg.de .In addition, the alternative optima space sample generated in this study can be requested under the same e-mail addresss.