# 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](https://gsmm.readthedocs.io/en/latest/).
## 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](https://github.com/KarthikDani/PHCCOProject/blob/main/gsmm/LICENSE.txt).
---
Raw data
{
"_id": null,
"home_page": "https://github.com/KarthikDani/PHCCOProject/tree/main/gsmm",
"name": "gsmm",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.7",
"maintainer_email": null,
"keywords": null,
"author": "Karthik Dani",
"author_email": "karthikdani14@gmail.com",
"download_url": "https://files.pythonhosted.org/packages/b0/a1/47836527283cc1b0336ad892b467e5c1698dc6566394eb18287a4e71d0b2/gsmm-0.1.9.tar.gz",
"platform": null,
"description": "# GSMM \n## An Open Source Tool for Building and Analysing Context Specific Metabolic Models and Generate visualisations.\n\n## Overview\n\nGSMM 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.\n\n## Features\n\n- **Model Integration:** Create Context Specific Metabolic Models with easy to use functions\n- **Flux Analysis:** Analyze and visualize flux distributions and correlations between metabolic models.\n- **Reaction Deletion Analysis:** Conduct reaction deletion studies and visualize results using cluster maps.\n- **Sink Flux Analysis:** Analyze and visualize sink fluxes for metabolites of interest.\n- **Visualization:** Generate high-quality plots for presentation and analysis.\n\n## Documentation\n\nFor detailed documentation of the source code, please visit [GSMM Documentation](https://gsmm.readthedocs.io/en/latest/).\n\n## File Structure\n\n```\ngsmm/\n\u251c\u2500\u2500 __init__.py\n\u2502\n\u2514\u2500\u2500 csm/\n \u251c\u2500\u2500 build_csm.py # Building metabolic models\n \u251c\u2500\u2500 analyse_csm.py # Analyzing metabolic models\n \u251c\u2500\u2500 visualisation.py # Visualizing analysis results generated from CSMs\n \u2514\u2500\u2500 config.py # Constants to store model paths, metabolites of interest, etc\n```\n\n## License\n\nThis project is licensed under the [MIT License](https://github.com/KarthikDani/PHCCOProject/blob/main/gsmm/LICENSE.txt).\n\n---\n",
"bugtrack_url": null,
"license": "MIT",
"summary": "Genome Scale Metabolic Modeling - [Currently] Pipeline for building and analyzing context-specific metabolic models",
"version": "0.1.9",
"project_urls": {
"Homepage": "https://github.com/KarthikDani/PHCCOProject/tree/main/gsmm"
},
"split_keywords": [],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "4c7f8beebdabcd9b15466bcc25d97a8be5636f410548c98ab3bb4b949093f8b9",
"md5": "e2c914057618c2cad584657ebb4ea9ff",
"sha256": "796379d86bdb41763db3aad90d0e31aba4847991631e001dfb9ca7f0b3e6d26a"
},
"downloads": -1,
"filename": "gsmm-0.1.9-py3-none-any.whl",
"has_sig": false,
"md5_digest": "e2c914057618c2cad584657ebb4ea9ff",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.7",
"size": 15028,
"upload_time": "2024-07-09T17:59:38",
"upload_time_iso_8601": "2024-07-09T17:59:38.101375Z",
"url": "https://files.pythonhosted.org/packages/4c/7f/8beebdabcd9b15466bcc25d97a8be5636f410548c98ab3bb4b949093f8b9/gsmm-0.1.9-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "b0a147836527283cc1b0336ad892b467e5c1698dc6566394eb18287a4e71d0b2",
"md5": "b33cfd17f8855f7fa82ccdde5518179d",
"sha256": "6556f9815583258d6424a1655b04160d930fdf2057b792515b4ca6bfe2bd7f52"
},
"downloads": -1,
"filename": "gsmm-0.1.9.tar.gz",
"has_sig": false,
"md5_digest": "b33cfd17f8855f7fa82ccdde5518179d",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.7",
"size": 14353,
"upload_time": "2024-07-09T17:59:39",
"upload_time_iso_8601": "2024-07-09T17:59:39.790578Z",
"url": "https://files.pythonhosted.org/packages/b0/a1/47836527283cc1b0336ad892b467e5c1698dc6566394eb18287a4e71d0b2/gsmm-0.1.9.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-07-09 17:59:39",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "KarthikDani",
"github_project": "PHCCOProject",
"travis_ci": false,
"coveralls": false,
"github_actions": false,
"lcname": "gsmm"
}
JSON
