A graphical editor for the reconstruction, annotation and testing of genome-scale models
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GEMEditor
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README.rst

Build Status Coverage Status PyPI

GEMEditor

GEMEditor as graphical user interface intended at the easy editing of genome-scale metabolic models. It has been written in an attempt of being able to integrate the biological information into a consistent metabolic model referencing the original data being used for reconstruction. GEMEditor is built on top of cobrapy which is used for model solving. The escher package is used for the visualization of solutions.

Installation

You can download and install the latest version of GEM Editor from pip.

Installation:

pip install GEMEditor -r requirements.txt

Updating GEMEditor:

pip install GEMEditor --upgrade

Usage

Run:

python -m GEMEditor.run [options]

Options

--debug
Run in debug mode for detailed logging
--file
Path to model