Tool: Pathomx - Workflow-based analysis software with metabolomics toolkit
gravatar for Martin Fitzpatrick
2.9 years ago by
Universiteit Utrecht
Martin Fitzpatrick40 wrote:

Pathomx is a workflow-based analysis tool featuring a NMR toolkit allowing rapid, reproducible and adaptable analysis of metabolomics data.  It was developed as part of my PhD in metabolomics of inflammatory diseases, where I found a need for a tool to enable higher-throughput reproducible analysis and aid interpretation of findings in biological context.

Pathomx visual editor

Workflows as constructed by a drag-drop interface from the toolkit. Each tool can be independently configured, and outputs are recalculated on the fly. Input is supported from pre-processed or raw Bruker NMR (other formats can be added on request), spectra can be processed for baseline correction, alignment (including icoshift) and normalisation (TSA, PQN). Peak assignments can be performed using online services or manual peak-match files (e.g. exported from Chenomx) and identified metabolites mapped to database entities using BioCyc, HMDB or other identifiers. Pathomx includes a pathway mining and automated visualisation tool to visualised most-regulated pathways, as well as support for more traditional views using GPML/WikiPathways or KEGG pathways.

Pathomx is fully extendible with the ability to create custom tools to perform new tasks, and allows manual editing of tool scripts to customise processing if needed. Workflows can be saved, shared and re-used, and all outputs/figures can be saved as high-resolution TIF for publication.

The current latest version is v3.0.2 (Released 26th October 2014) available as download for Windows and Mac.

Documentation is available and a quick video showing 1D NMR analysis with Pathomx.

If you have any questions, comments or suggestions please let me know!

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

ADD COMMENTlink modified 2.7 years ago • written 2.9 years ago by Martin Fitzpatrick40

I would suggest to use MetaStars to provide support for the tool instead of a mailing list. You can watch a tag in your user profile. The site will send you an email when a post with the tag gets posted.

Quite a few tools are supported via Biostars for example.

ADD REPLYlink written 2.9 years ago by Istvan Albert ♦♦ 90

Great suggestion, thanks. I've updated the documentation to add MetaStars (and BioStars) as options for support.

ADD REPLYlink written 2.9 years ago by Martin Fitzpatrick40
gravatar for Andrew Patterson
2.9 years ago by
Penn State University
Andrew Patterson180 wrote:

Thanks for post Martin. This is fantastic resource and one that we are likely to try since we are using more NMR as part of our metabolomics approach. Have you published a paper with this tool?

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Andrew Patterson180

Thanks Andrew, let me know how you get on. I've submitted a paper for the software and it's currently under review, will update the post once it is published. [The paper is now published; I've updated the post]

ADD REPLYlink modified 2.7 years ago • written 2.9 years ago by Martin Fitzpatrick40
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