Re: Aw: Bioinformatics course in debian-med - feasibility?
Hi Steffen, Christoph, Yaroslav, Tony and Charles,
I very much like the idea of helping debian-med on ARM in some way. Some
of our 4273pi Bioinformatics for Biologists exercises could be scripted,
so presumably would work as regression tests. We often don't know the
'real' result but can get the result on AMD64, and check for deviation
from that.
Entirely agreed: the Raspberry Pi is not powerful. Somewhere between a
Cray 1 and a Cray 2, and with 512 GB RAM. Tony's Parallella will be
enormously more powerful and will be great to see.
Our teaching on Pi uses full 'industrial-strength' analyses, but on small
input. We have not yet used the Pi for genome assembly. Others have:
https://twitter.com/richardmleggett/status/211944292128796672
http://hal.inria.fr/hal-00842027
The 4273pi Bioinformatics for Biologists course does not currently use
strap. (It uses Clustal-X, not for aligning but for previewing a multiple
alignment generated by MAFFT.) We have someone lined up to improve
coverage of multiple alignment in the future - I'm not sure what he'll use.
Agreed: At this stage we do not have to be extremely detailed about what
distribution to contribute to. I am happy to leave this somewhat open for
now.
Regarding BioLinux possibilities: Ubuntu does not run on the Pi (ARM11 /
ARM v6). It does run on the somewhat faster and more expensive Cotton
Candy (Cortex-A9, ARM v7,
http://www.fxitech.com/cotton-candy/what-is-it/). I will soon own one of
these. But irrespective of all this, we absolutely want our future
teaching material to be able to 'slot into' BioLinux and will make sure
that it fits.
Thank you - this conversation has been exceptionally useful, I'm learning
a lot.
Best wishes,
Daniel
--
Daniel Barker
http://biology.st-andrews.ac.uk/staff/db60
The University of St Andrews is a charity registered in Scotland :
No SC013532
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