Monday, 27 October 2014

Custom Scripts

Quite often a biologist will come to me with a paper and ask me to recreate an analysis on their data.

"Sure", I say, and start to skim through the methods for the bioinformatics section.

.. were upregulated blah blah ... <PageDown>
... p<0.001 ... <PageDown>
... Cultivated blah blah nanomolar ... <PageDown>
"were sequenced on" (ok here it is) ... "analysed with custom bioinformatics scripts" ....

And there it is, the rage again!

Custom scripts! Of course! It's all so clear now!

What "custom scripts" (and only custom scripts) in your methods tells me is you did something critical to produce your results, and you won't tell me how or what.

So by now I've long stopped thinking about your experiment, and am now wondering what was going on in your head to make you think this is acceptable.

Are all programs the same to you? So stupefyingly dull that they are not worth more than a few words to describe? A mere matter of programming, how could it be wrong! Or is it the other way? Code is magical, mysterious and beyond human comprehension?

Or maybe you think all science should be written up like this?

Microscopy advances summarised as "custom optical methods". PCR written up in the 80s as "DNA was copied using custom molecular biology methods"? Assays as custom measuring methods, antibodies - custom rabbit methods?

Oh, and people that write "Custom Python", "Custom Perl" or "Custom R Scripts" as if that makes it better?

Thanks, now I know what language the code you're not showing me is written in? Fuck you with custom Fucking methods!

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