A Qiime 2 plugin for MICOM.
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
conda install -c bioconda -c conda-forge cobra umap-learn jinja2 pyarrow tqdm
q2-micom (this will install
MICOM as well).
pip install git+https://github.com/micom-dev/q2-micom
Install a QP solver
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
Now install the CPLEX python package:
pip install ibm/cplex/python/3.6/x86-64_linux
x86-64_linux with the folder corresponding to your system.
Gurobi can be installed with conda.
conda install -c gurobi gurobi
You will now have to register the installation using your license key.
You are now ready to run
Here is a graphical overview of a
The best way to get started is to work through the community tutorial.
MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota
Christian Diener, Sean M. Gibbons, Osbaldo Resendis-Antonio