[IPython-dev] Pathomx: Workflow-based data analysis built on IPython notebooks

Martin Fitzpatrick martin.fitzpatrick at gmail.com
Tue Jun 24 08:10:05 EDT 2014


Hello all

Following up on QtIPy here is another software-release that I think may be
of interest to the list: Pathomx v3.0.0a - a workflow-based data analysis
application that is (as of now) built on IPython notebooks.

A short bit of history: Pathomx has been under development for a year or so
as a desktop-based data analysis platform using drag-and-drop analysis
workflow construction. It was developed alongside my PhD to provide a way
both to alternate analysis approaches quickly and have reproducible
analysis. A few months ago I discovered IPython (+notebooks) and saw the
great potential there for reproducibility, but still missed the automation
and prototyping available from Pathomx. So I did the obvious thing and
combined them.

Here is a short demo video of it in action -
http://www.youtube.com/watch/L5HxshxH67o

With Pathomx you can now -

* Build workflows using IPython-notebook based tools
* Auto-display in the GUI of Matplotlib figures and pandas dataframes from
workbooks
* Auto-export of (selected) variables from workbooks to pass to other tools
* Export figures, set standardised plot colors, etc. from within the GUI
* Save and reload workflows to share analysis
* Export completed workflows to compound IPython notebooks to run
independently

There are two expected use-cases - a) non-programmers to construct analysis
workflows from standardised components provided b) rapid prototyping of
different analysis approaches for export as completed standalone noteboks.
I think this latter one is particularly neat.

There are a few issues to address before a full release including hopefully
switching to a Qt-aware kernel (it's built on PyQt5 which as I understand
it isn't currently supported - but I'll work on that).

Source available here: https://github.com/pathomx/pathomx

Requires PyQt5 and then pip install numpy pandas scipy  matplotlib  biocyc
pyqtconfig mplstyler yapsy runipy

Feedback, comments and suggestions are most welcome

Martin
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