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A Qiime plugin for MICOM.
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A Qiime 2 plugin for MICOM.

Installation

This will become easier soon.

Setup Qiime 2

You will need a Qiime 2 development environment (install Qiime 2). Once installed, activate the environment:

conda activate qiime2-dev

Install dependencies for q2-micom:

conda install -c bioconda -c conda-forge cobra umap-learn jinja2 pyarrow tqdm

Install q2-micom (this will install MICOM as well).

pip install git+https://github.com/micom-dev/q2-micom

Install a QP solver

Finally, MICOM requires a quadratic programming solver. We currently support CPLEX or Gurobi, which both have free academic licenses but will require you to sign up for them.

CPLEX

After registering and downloading the CPLEX studio for your OS unpack it (by running the provided installer) to a directory of your choice (we will assume it's called ibm).

Now install the CPLEX python package:

pip install ibm/cplex/python/3.6/x86-64_linux

Substitute x86-64_linux with the folder corresponding to your system.

Gurobi

Gurobi can be installed with conda.

conda install -c gurobi gurobi

You will now have to register the installation using your license key.

grbgetkey YOUR-LICENSE-KEY

You are now ready to run q2-micom.

Usage

Here is a graphical overview of a q2-micom analysis.

The best way to get started is to work through the community tutorial.

References

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota
Christian Diener, Sean M. Gibbons, Osbaldo Resendis-Antonio
mSystems 5:e00606-19
https://doi.org/10.1128/mSystems.00606-19

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