Pathomx is a workflow-based tool for the analysis of metabolic pathways and visualisation of associated experimental data. Create workflows, edit and share 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.
The latest alpha is built on IPython Notebooks allowing construction of workflows from re-useable scripts. Prototype workflows in Pathomx with drag and drop construction and export completed scripts.
For latest updates follow @pathomx on Twitter.
We’re making demos of Pathomx in use. If you have a video showing off your own analysis, or demo datasets and workflows you’d like to share send us the link and we’ll list it here.
Pathomx started as a metabolomic-analysis platform, and so naturally many of the bundled tools are still geared towards this. The integrated BioCyc database, MetaViz metabolic pathway visualisation tool and support for GPML, WikiPathways, KEGG and more make Pathomx ideal for biological data analysis.
Visualise your data using matplotlib and d3.js. Generate figures using your own notebooks or the included libomx helpers and then interact with them in the GUI figure editors.
You can save and export figures easily, and manage appearance settings across all figures centrally through the configuration tools.
Pathomx is available free for any use, licensed under the GPLv3. Helper modules and functions are all released under MIT or BSD licensing and can be shared without restrictions.
IPython notebook-based tools contain all you need to know to use them simply open up a tool within Pathomx and read away.
Installable binaries are available currently for Mac OS X and Windows.
Previous releases are also available for download if required:
We’re actively looking for Pythonistas to help make Pathomx more awesome. Any level or experience welcome, don’t be shy.
Even easier is contributing IPython Notebooks for custom analysis tools. There isn’t much documentation on this at the moment but check out the bundled tools to see how it all works.
For more information on Pathomx, development etc. please contact me at:
℅ Centre for Translational Inflammation Research
Queen Elizabeth Hospital
University of Birmingham