GradDescMicrobiota is a repository that contains a modified version of µbialSim, which was originally published in "Popp, D. and F. Centler. 2020. “µbialSim: Constraint-Based Dynamic Simulation of Complex Microbiomes.”, Front. Bioeng. Biotechnol. 8 (June): 574. https://doi.org/10.3389/fbioe.2020.00574.". The original toolbox is licensed under the GNU General Public License v3.0. This modification includes a Gradient descent algorithm that allows the user to replicate relative abundance microbial community compositions.
When using GradDescMicrobiota please cite the following: ""
The modifications made to the original toolbox are:
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Original scripts needed to run the examples found in https://git.ufz.de/UMBSysBio/microbialsim/-/blob/master/microbialSimMain.m have been removed, insted a script named "mainGradDesc.m" has been added to include the Gradient descent optimisation algorithm. This file is the main script to run the modelling scheme.
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The following files have changes attached to them which are specified as comments in the script:
- prepareFBAmodel.m
- dFBASimulator.m
- reactorDefinition.m
- microbialSim.m
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Most of the code required to employ CellNetAnalyzer have been removed from the scripts. However, downloading the original files from the µbialSim toolbox, CNA can still be used.
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This modified toolbox requires:
- COBRA Toolbox for FBA computations.
-Information on the COBRA Toolbox is available here:
https://opencobra.github.io/cobratoolbox/stable/index.html
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To install and start using the modified toolbox, information is provided in the original publication's code (https://git.ufz.de/UMBSysBio/microbialsim).
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The main file to use the modelling scheme is: mainGradDesc.m
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The following files require user input in order to contextualize the framework to an specific model system: mainGradDesc.m microbialSimMain.m prepareFBAmodel.m reactorDefinition.m
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Files are included for the nutritional space used in the simulations (Unhealthy.txt & DMR38.xlsx). The unhealthy.txt is a .txt version of the diet with the same name which can be obtained from https://www.vmh.life/#nutrition.
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Metabolic reconstructions for recreating the simulations of the original publication are included in the assets of this repository. In addition to this AGORA reconstructions are available in: https://www.vmh.life/#downloadview
- M.Sc. Juan Ricardo Velasco Álvarez, UPIBI, IPN. -PhD. Jorge Isaac Chairez Oria, Tecnólogico de Monterrey, Campus Guadalajara
Contact:
This modified toolbox is licensed under the GNU General Public License v3.0. A copy of the license is included in this repository.