MetaPath v0.6.0 Released

An update has been released today for MetaPath, a metabolic pathway visualisation and analysis tool. It is available via PyPi and github. A Mac .app bundle is also available.

Screenshot

Download Mac OS X Mountain Lion .appGithubPython .egg or .gz.

MetaPath requires installation of Graphviz for pathway drawing.

More background on the software is given in the original release announcement.

What’s new?

This latest release of MetaPath brings a number of useful new features for both data analysis and educational uses, together with a number of bug fixes and stability improvements. As always, feedback and bug reports are appreciated!

Screenshot

Compartmentalisation: MetaPath is now aware of reaction compartamentalisation, as derived from BioCyc protein localisation data. Using this data, it is now possible to draw overviews of reaction locations within the cell and use this to guide analysis. Compartment-based scoring will be introduced in later versions.

Screenshot

Metabolite structure images: Built with permission from KEGG metabolite structure data. You can now visualise reactions with metabolite structure images to see actual molecular changes taking place at each step. Images can also be coloured for data analysis purposes. Atom-tracking is the eventual goal, of particular use in metabolic flux experiments.

Screenshot

GPML (WikiPathways) support: Based on my recent work on gpml2svg, MetaPath now supports GPML natively and can display GPML marked up pathways within the application. Data visualisation is not currently supported (it is present in the underlying gpml2svg code, but needs a bit of work translating database identifiers).

What’s next?

Current plans include data visualisations on GPML format pathways (including longitudinal analysis to match MetaCyc pathway capabilities), data analysis and visualisation tools including graphing, heatmaps and other meta-summaries of metabolite changes (oxidative state, ATP-ADP balance, etc.), support for data input, annotation and display (spectra, peak picking, etc.). Look out for updates!


Discussion

Related posts

Get my latest Python projects, tips & tutorials direct to your Inbox.