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[OT] Re: Guix and Bioconductor.

From: Giovanni Biscuolo
Subject: [OT] Re: Guix and Bioconductor.
Date: Sat, 21 Dec 2019 11:06:22 +0100

[A quick and dirty off topic rant... forgive me!]

Hello Ricardo,

thank you for the info!

...and thank you all for working on resolving this class of problems
through Guix!

Ricardo Wurmus <address@hidden> writes:

> Giovanni Biscuolo <address@hidden> writes:


>> I fear flowPeacks will not be the last package with this kind licensing
>> problems
> It sure isn’t.  In the past I have tried to do a mass import from
> Bioconductor and what slows me down the most is incorrect or non-free
> licensing.  There are some packages that declare to be licensed under
> Artistic 2.0, but then actually they contain data from databases that
> do not permit commercial use.  Or they contain a copy of non-free tools,
> or only work when those tools are present (e.g. kent tools, of which we
> provide a package containing the few free tools).

This confirms that licensing is an integral part of reproducibility and
replicability, unfortunately a very neglected part even in academia (not
to mention "industry") :-( .  This is also part of the current science
crisis... OK stop ranting :-D

> It’s a pretty frustrating process to weed out these packages.

Let them know! (Do they know?)

«Dear Bioconductor Team, you state you are committed to bla bla
reproducible research but *some* of the research you host is
unreproducible for the simple reason some authors are ignoring licensing

>> Since «Bioconductor is committed to open source, collaborative,
>> distributed software development and literate, reproducible research.» [1]
> CRAN appears to be stricter about licenses (even though “strict” is
> probably much too strong a word…).  Bioconductor people appear to care a
> little less.

I'm out from academia, but every time I talk to friends involved in
academia I'm pretty astonished by the general lack of scientific method
[1] [2] applied in academia :-O.  A little bit of metascience would help.

...and more Guix in academia is part of the solution :-D

Thanks! Gio'

«In 2016, Nature conducted a survey of 1,576 researchers who took a
brief online questionnaire on reproducibility in research. According to
the survey, more than 70% of researchers have tried and failed to
reproduce another scientist's experiments, and more than half have
failed to reproduce their own experiments.»


Giovanni Biscuolo

Xelera IT Infrastructures

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