[IPython-dev] QtIPy: The IPython Notebook-based data automator

Martin Fitzpatrick martin.fitzpatrick at gmail.com
Thu May 15 07:11:30 EDT 2014

Thanks Thomas

On 14 May 2014 17:23, Thomas Kluyver <takowl at gmail.com>wrote:
> Thanks for letting us know about this, it looks really interesting. Can
> tell us a bit about the problem you wrote it to solve? I imagine it's
> something like preparing reports from data that's regularly updated, but
> would be good to hear some more detail.

Scientific data analysis typically includes a lot of routine steps. For
example in metabolomics (what I do) from the raw NMR data you typically
phase correct, baseline correct, normalise, bin, and then do some kind of
multivariate analysis (PCA or PLS-DA) to see if you've got anything of
interest. Most of these steps can be automated as a 'good enough, first
look' and so I wanted a way to quickly apply these steps together while
getting a record of what was done - preferably by doing nothing more than
drag-dropping a file into a specific folder.

Doing it in an IPython notebook has the added benefit of
inline-documentation of everything - which is incredibly useful when
sharing processing approaches. I can now write a processing script, give it
to a non-expert to run against data, and they get the processed outputs
together with a nicely formatted report of how it happened. I think that's
a great educational/transparency tool.

I wrote it as an automator, but some additional features (per-automaton
variables and configuration, including a manual-run config panel) are

> Please do add it to the list of projects using IPython:
> https://github.com/ipython/ipython/wiki/Projects-using-IPython


Thanks again.

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