Projects / Pathomx


Pathomx is a workflow-based tool for the analysis of metabolomic and other omics datasets. It is interactive, visual, extensible, intelligent, and free for any use. It lets you dynamically build analysis workflows using the interactive editor. Drag and drop connections between plugin tools to create a complete workflow through which to run your analysis. Data can be loaded and processed automatically, and new approaches tested simply by connecting tools.

Operating Systems

Recent releases

  •  30 Apr 2014 22:45

    Release Notes: Annotations for the workflow editor allow you to mark areas of the workflow and add descriptive notes. Snap to grid, show/hide grid, and workflow-image export. Improvements to spectra-plot annotations. Support for European-style semicolon-delimited CSV and format auto-detection. Legacy tool import filters allowing modified tools to provide a backwards-compatible interface for loading. Fixes for PCA/PLS-DA on >2 components.

    •  14 Apr 2014 19:15

      Release Notes: Improved figure outputs and interactive plots (zoom, pan). Sample class line-style and marker-style tools keeping plots consistent throughout. MATLAB and R integration: run scripts on your locally installed MATLAB/R platforms directly from within Pathomx.MATLAB data export: export datasets directly to MATLAB format workspace files. NMRLab integration. Experimental native wrappers for MATLAB-based NMR processing tools (requires MATLAB). Numerous bugfixes and improvements; increased processing speed.

      •  08 Feb 2014 14:18

        Release Notes: This release adds a new name, Pathomx, reflecting pathway-centered analysis of multi-omics data, interactive figures allowing for zooming and panning through displayed datasets, sidebar panels allowing easier configuration of tool settings with on-the-fly recalculation, and a selection of new tools, including baseline correction and autophasing for NMR spectra.

        •  13 Jan 2014 18:11

          Release Notes: 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).

          •  17 Dec 2013 17:08

            Release Notes: This version adds a number of important features over the previous release. It has multi-threaded processing, allowing multiple analysis steps to be performed in parallel to speed up your analysis. There is an online plugin repository with a built-in installation and update system. There is Windows 7 & 8 (x64) and Mac OS X support.


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