Pathomx

Software Screenshot:
Pathomx
Software Details:
Version: 3.0.0a
Upload Date: 17 Feb 15
Developer: Martin Fitzpatrick
Distribution Type: Freeware
Downloads: 12

Rating: nan/5 (Total Votes: 0)

Pathomx (formerly MetaPath) is an open source graphical software implemented in IPython, Qt and PyQt, designed from the ground up to act as an interactive utility for the visualization and analysis of metabolic data under GNU/Linux and other POSIX operating systems. It was initially engineered to be used for processing metabolomics data.

Features at a glance

Key features include support for importing and exporting NMR (Nuclear Magnetic Resonance) data, spectra processing, including normalization, binning and alignment, as well as metabolic pathway visualization and mining. You will also be able to import genomic and metabolomics data through various routes for visualisation on specified pathways.

Various MetaCyc database annotations are also included in the Pathomx application, among which we can mention database unification links, synonyms, as well as associated pathways and reactions. Please note that the MetaCyc database is derived from the public API.

The application uses the powerful MetaCyc database for rapid exploration of complex datasets, thanks to extensible and configurable plugins. In addition, it uses the Numpy and Scipy libraries for number handling, Matplotlib for graphing, nmrglue for NMR data import, d3.js for interactive graphs, and scikit-learn for statistical analysis methods.

Under the hood and supported OSes

Looking under the hood of Pathomx, we can notice that the application has been built on IPython command shell. It also works well under Microsoft Windows and Mac OS X operating systems, for which it is available for download as pre-built binary packages. For GNU/Linux, the software is distributed only as a gzipped source archive compatible with 32-bit and 64-bit hardware platforms.

When using Pathomx, users should keep in mind that the application makes use of data from the MetaCyc pathway database itself, which is part of the BioCyc family. The MetaCyc API is used to generate the supplied database, which is stored locally.

What is new in this release:

  • A completely new drag-drop visual editor was added.
  • It allows you to create analysis workflows by dragging tools into the workspace, editing connections by dragging data lines between tools, and using inline views to get an overview of current processing.
  • Data can be dropped into the workspace for instant import.
  • It also added live per-tool progress notifications, bars, and status indicators.
  • Errors are flagged with help text (tooltips on tools when indicated red).

Requirements:

  • Graphviz

Similar Software

Jmol
Jmol

22 Jun 18

NetAtlas
NetAtlas

2 Jun 15

E-Cell System
E-Cell System

11 May 15

Other Software of Developer Martin Fitzpatrick

Pathomx
Pathomx

8 Dec 14

Pathomx
Pathomx

22 Nov 14

Comments to Pathomx

Comments not found
Add Comment
Turn on images!