micom
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micom-dev
Python package to study microbial communities using metabolic modeling.
This improves the Gurobi support in MICOM by adjusting the numerical handling and explicit use of faster primal accessors. ## Changes - follow the best practices from the [Gurobi Numerical...
### Discussed in https://github.com/micom-dev/micom/discussions/69 Originally posted by **anubhavdas0907** March 8, 2022 Hello Christian, I was trying to copy a community model to a different variable, but I get an error....
This is a proposal for a new format for fluxes slated for MICOM 1.0. Feel free to comment :smile: ### Checklist - [X] There are [no similar issues or pull...
### Checklist - [X] There are [no similar issues or pull requests](https://github.com/micom-dev/micom/issues) for this yet. - [X] The request is *not* specific for MICOM Qiime 2 plugin (q2-micom) ### Bundled...
### Checklist - [X] There are [no similar issues or pull requests](https://github.com/micom-dev/micom/issues) for this yet. - [X] The request is *not* specific for MICOM Qiime 2 plugin (q2-micom) ### Is...
### Checklist - [X] There are [no similar issues or pull requests](https://github.com/micom-dev/micom/issues) for this yet. - [X] The request is *not* specific for MICOM Qiime 2 plugin (q2-micom) ### Is...
The format for the taxonomy table community model manifests can be unclear and both are often confused for one another. Provide a validation helper and better error messages.
When using models from different sources metabolite IDs may not be matched. Mention this pitfall in the docs and implement a warning in case models have no (or little) shared...
# Purpose The former strategy of identifying metabolite:phenotype associations with coefficients from a LASSO models has proven to be quite unstable due to (a) the non-uniqueness of the coefficients and...
# Purpose This adds functionality to analyze metabolic interactions in already existing outputs from the `grow` workflow. Functionality is added in the new `micom.interaction` module and the extended visualizations that...