modelling gut bacteria - Githubissues

opencobra / cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

https://opencobra.github.io/cobratoolbox

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modelling gut bacteria #1691

Open bab135 opened 3 years ago

bab135 commented 3 years ago

Please include a short description of problem here how to get codes for developing community modelling of probiotics in MATLAB. also how to simulate this in recon 3d ? I hereby confirm that I have:

[x ] Tried to solve the issue on my own
[ ] Retried to run my code with the latest version of The COBRA Toolbox
[ ] Checked that a similar issue has not already been opened

(Note: You may replace [ ] with [X] to check the box)

almut-heinken commented 3 years ago

Hello, if you have metagenomic or 16S rRNA data, you can create sample-specific community models from AGORA using the Microbiome Modeling Toolbox. https://github.com/opencobra/cobratoolbox/tree/master/src/analysis/multiSpecies/microbiomeModelingToolbox Otherwise, you can use the function createMultipleSpeciesModel to build a defined model. In both cases, the microbiome models can be readily combined with Recon3D. Best regards, Almut