gsmm 0.1.9

Genome Scale Metabolic Modeling - [Currently] Pipeline for building and analyzing context-specific metabolic models

GSMM

An Open Source Tool for Building and Analysing Context Specific Metabolic Models and Generate visualisations.

Overview

GSMM is a Python-based toolkit for Genome Scale Metabolic Modeling, designed for [currently] analyzing and visualizing metabolic models during my PHCCO Internship, specifically tailored for integrating transcriptomics based expression data and conducting nutrient depletion studies [ongoing]. It utilizes computational biology techniques to analyze flux distributions, reaction deletions, and sink fluxes across context-specific metabolic models.

Features

• Model Integration: Create Context Specific Metabolic Models with easy to use functions
• Flux Analysis: Analyze and visualize flux distributions and correlations between metabolic models.
• Reaction Deletion Analysis: Conduct reaction deletion studies and visualize results using cluster maps.
• Sink Flux Analysis: Analyze and visualize sink fluxes for metabolites of interest.
• Visualization: Generate high-quality plots for presentation and analysis.

Documentation

For detailed documentation of the source code, please visit GSMM Documentation.

File Structure

gsmm/
├── __init__.py
│
└── csm/
    ├── build_csm.py                  # Building metabolic models
    ├── analyse_csm.py                # Analyzing metabolic models
    ├── visualisation.py              # Visualizing analysis results generated from CSMs
    └── config.py                     # Constants to store model paths, metabolites of interest, etc

License

This project is licensed under the MIT License.

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