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GraphCM

A new method for processing of currency metabolites in metabolic networks based on graph theory

About

The pipeline was written and tested with Python 3.8. The core libraries essential for the pipeline including: Cobra, Pandas, networkx, and related packages.

Installation

  1. create bow_tie environment using conda:
$ conda create -n graph_CM python=3.8
  1. install related packages using pip:
$ conda activate graph_CM
$ pip install cobra
$ pip install networkx
$ pip install ipykernel
$ python -m ipykernel install --user --name graph_CM --display-name "graph_CM"

Steps to reproduce the analysis in the publication

Download all data and analysis code from github (directlt download or use git clone).

$ cd /file path/project save path/
$ git clone https://github.com/tibbdc/GraphCM.git

All results can be reproduced by executing the Jupyter Python notebooks:

  • graph_currency_metabolites.ipynb
    • the main script of removing currency metabolites based on graph theory approach.