q2-micom 0.7.1

Plugin for metabolic modeling of microbial communities.

A Qiime 2 plugin for MICOM.

Installation

This will become easier soon.

Setup Qiime 2

You will need a Qiime 2 environment with version 2020.2 or higher (how to install Qiime 2). For instance on Linux you would use:

wget https://data.qiime2.org/distro/core/qiime2-2020.2-py36-linux-conda.yml
conda env create -n qiime2-2020.2 --file qiime2-2020.2-py36-linux-conda.yml
# OPTIONAL CLEANUP
rm qiime2-2020.2-py36-linux-conda.yml

Once installed, activate your Qiime 2 environment:

conda activate qiime2-2020.2

Install dependencies for q2-micom from conda:

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

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

pip install q2-micom

Install a QP solver

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 (there will only be one subfolder in that directory).

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

Finish your installation

If you installed q2-micom in an already existing Qiime 2 environment, update the plugin cache:

conda activate qiime2-2020.2  # or whatever you called your environment
qiime dev refresh-cache

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