A metabolic modeling workflow for communities of organisms in an nasal medium. This implements functionality to analyze the interaction of metabolic models within a community.

Authors: Manuel Glöckler, Reihaneh Mostolizadeh

Full documentaion page: https://manuelgloeckler.github.io/ncmw/

Repository: https://github.com/manuelgloeckler/ncmw

Citation: Please cite us

[1] NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome https://www.frontiersin.org/articles/10.3389/fbinf.2022.827024/full

[2] Towards the human nasal microbiome: Simulating D. pigrum and S. aureus https://www.frontiersin.org/articles/10.3389/fcimb.2022.925215/full

Please see the full documentation as a user manual at https://manuelgloeckler.github.io/ncmw/

Please clone the repository using git clone https://github.com/manuelgloeckler/ncmw.git . The package and all the dependencies can be installed via pip. The only requirement that is not installed is some solver that can minimize quadratic objectives and is supported by Pycobra. This is for example "cplex", which can be installed via pip install cplex, but requires a license (required for COOPM analysis).

After having cloned the repository, please enter the following command in the same directory where the cloned repository is located:

pip install -e ncmw

This will install the python package ncmw but also console scripts ncmw_setup, ncmw_analysis, ncmw_community, and ncmw, which calls the latter three scripts in sequential order.

These scripts use hydra, thus we can overwrite all default values which are organized within data/hydra. More on overwriting arguments in scripts_

NOTE: Automatically adding scripts to the PATH may not work if the python environment is not set up correctly. Alternatively you can call the scripts by python scripts/ncmw_setup

These should be added to your PATH environment variable, to try if this worked use:

ncmw --help ncmw_setup --help ncmw_analysis --help ncmw_community
     --help

It might be necessary to have advanced user permissions because the installation script may write into a central directory within your operating system. If you receive an error during the installation procedure on a computer running macOS, you may need to create an empty file /usr/local/LICENSE with write permissions by typing

sudo touch /usr/local/LICENSE
sudo chown $(whoami) /usr/local/LICENSE

Now rerun pip install -e ncmw and it should work. If not, please report your problem via the issue tracker.

The package is organised into five parts:

• setup_models: which setup metabolic models to the given default configuration and medium, e.g., typically SNM3.
• analysis: which contains all function for single model analysis .
• community: which contains all code for community analysis and implemented community models.
• visualization: which contains all code to produce figures.

The data folder can be used to modify default values:

• configs contains the default settings for the maximum lower and upper bound of reactions, which is -1,000 and 1,000 mmol/gDW/h.
• hydra contains all default parameters for the scripts, which can be overwritten in the console.
• medium contains the default SNM3 medium.
• models contains all models that are used by the scripts.

You can change the default values if needed or add additional models to the workflow.

The scripts will automatically produce some results, that is:

• ncmw_setup:

• Will set the default bounds as specified in data/configs, as well as the medium as specified in data/medium.

• Will “gapfill” the model with reactions or the medium with metabolites, such that all models obtain growth on the specified medium

• ncmw_analysis

• Will perform flux variability analysis and visualize results on all exchange reactions.

• Will analyze the uptake/secretion overlap between models

• Will compute the similarity of models, based on number of shared metabolites/reactions.

• Will compute the COMPM medium, which is the medium in which all models are able to obtain their maximal biomass rate.

• ncmw_community

• Will create several kinds of community models.

• Will compute the COOPM medium, which is the smallest medium such that the community achieves 10% of the maximal biomass rate, which induces cooperation.

• Will visualize the observed interactions between models.

• Will investigate the dependence of community weight and observed growth.

NCMW is Copyright (C) 2021-2022 by the following organization:

The University of Tübingen, Germany

NCMW is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation.