MetaPath: Metabolic pathway visualisation and analysis [Released]
MetaPath requires installation of Graphviz for pathway drawing.
Who’s it for?
MetaPath is developed as an ongoing part of my PhD to build analysis software for metabolic pathways that is user-friendly, intuitive, informative and quick. However, it is equally suited for educational purposes, particularly metabolic pathway exploration.
It is based on the MetaCyc database. If you use that, you might want to use this.
What does it do?
MetaPath has two key use-cases:
Metabolic pathway exploration: Browse through the metabolic pathway database, with automated clean rendering of pathways. Add and remove metabolic pathways, show intra-pathway linkages, and map metabolic routes through the system. Browse the in-built database, following links to online resources for further information.
Metabolic data visualisation: Load experimental data gathered by mass-spectroscopy (MS) or nuclear magnetic resonance (NMR) spectroscopy and visualise metabolic changes overlaid on a a map of the sytem. Visualise gene-expression or protein quantity data alongside to explore relationships between enzyme regulation and metabolic processes. Use the built-in “Pathway Mining” tools to select the most up, down, or overall regulated pathways in the given system to identify the key mechanisms at work.
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Nothing. It’s released open-source under the the GPLv3 license and is therefore free to use for whatever purposes you wish. You can clone the repository, download Python .egg or .gz or download a built Mac app. Builds for other platforms will follow shortly.
MetaPath is built on the MetaCyc pathway database itself part of the BioCyc family. The supplied database is generated via the MetaCyc API and stored locally. Licenses for the entire MetaCyc database are also available free of charge for academic and government use.
Contributions from users and developers at other institutions are most welcome. Fork the repo on github. If you have issues, bugs or feature requires please report them and I’ll do what I can. Finally, if you have any questions drop a note in the comments below.
- MetaPath v0.6.0 Released
- MetaPath v2: Visual analysis for metabolomics [Released]
- Pathomx v3.0.0alpha4 for Mac
- Pathomx (née MetaPath) v2.2.0 released
- Pathomx v3.0.0 Release Candidate 2
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