Tool: Pathomx: Metabolic Pathway Visualisation And Analysis
gravatar for Martin Fitzpatrick
7.5 years ago by
Birmingham, United Kingdom
Martin Fitzpatrick180 wrote:

What is Pathomx?

Pathomx is a workflow-based metabolomics analysis tool. It has been developed as part of my PhD to enable rapid visualisation and interpretation of metabolic data within a pathway context.


The latest release (v2.5) provides a number of novel features:

Workflow based data exploration: Workflows can be created, edited and shared using the built-in analysis workflow editor. Set up standardised analysis approaches and apply them to new data consistently. Add-remove tools to test different approaches, and re-apply tried and tested methods to new data.

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.

Pathomx 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.

It strives to be user-friendly, intuitive and quick - and not too shabby looking.

Download Windows 7 & 8 .msi InstallerMac OS X Mountain Lion .appGithub

Note: Pathomx requires installation of Graphviz for the automated pathway drawing.


pathomx is released open-source under the the GPLv3 license and is therefore free to use for whatever purposes you wish. You can clone the repository or download a built Windows 7 & 8 .msi Installer or Mac app.

Note: pathomx requires installation of Graphviz for some pathway-drawing elements.


Contributions and comments 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.

Citing pathomx

If you use Pathomx in your analysis please cite: MA Fitzpatrick et al. Pathomx: an interactive workflow-based tool for the analysis of metabolomic data BMC Bioinformatics 2014 doi:10.1186/s12859-014-0396-9

tool visualization python pathway • 4.7k views
ADD COMMENTlink modified 5.8 years ago • written 7.5 years ago by Martin Fitzpatrick180

I would like to try but the mac image doesn't work for me.

ADD REPLYlink written 7.5 years ago by Manu Prestat4.0k

Thanks for giving it a go Manu. What errors did you get? Did you install Graphviz ( beforehand? I'm working on removing that as a dependency but it's currently needed for the layout.

ADD REPLYlink written 7.5 years ago by Martin Fitzpatrick180

We have a new version of MetaPath ready for release and a publication following along shortly. Should I update (edit) this post or post a new entry? Thanks

ADD REPLYlink written 6.9 years ago by Martin Fitzpatrick180

That's a pretty neat application. Is it planned to include BLAST results at some point, for the same kind of analysis?

ADD REPLYlink written 6.7 years ago by David Westergaard1.4k

Yep David. I've written it from the ground up to be as 'generic' as possible. Each of the 'tools' you see in the workflow define the inputs they'll take, process them and output them. So far all the tools use a generic 'DataSet' object but implementing a data holder for BLAST data should be fairly trivial. I'm a metabolomic type myself, but I'm actively looking for people able to extend the feature-set to other -omics.

ADD REPLYlink written 6.6 years ago by Martin Fitzpatrick180

Yes, edit it please I would like to know how it works in detail. Thanks

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by Lluís R.950

Thanks Lluis. I've updated and extended it a bit - is there something in particular you're looking to know? There is a new website up at with a bit more information and I've started bulking out the API documentation for plugin-building. Any suggestions are most welcome.

ADD REPLYlink written 6.6 years ago by Martin Fitzpatrick180

We have recently deployed a Biostar Q&A for metabolomics. It is at an incipient stage, with long periods of no posts, like Biostar was maybe four years ago. But the team that I am working with is committed to jumpstarting it with more material over the summer.

I would recommend to post it there as well

ADD REPLYlink modified 9 months ago by RamRS30k • written 6.4 years ago by Istvan Albert ♦♦ 85k

I only just noticed your comment here Istvan. I've signed up for Metastars and will take a look! Thanks

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by Martin Fitzpatrick180
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