Re: about gsocs2013
Le Wed, Apr 10, 2013 at 10:46:30AM +0200, Nigi Fabio a écrit :
>
> i' m Fabio, master student @ university of Pisa in computer engineer
> i'd like to have more info about the project on wiki pages for the
> cloud image for bioinformatics with Debian
Dear Nigi,
I was deliberately vague when writing the description of the project for
bioinformatics on the Cloud using Debian, because I want this project to be
bottom-up, where the student particpates in the shaping of the proposal.
I have listed some frequent problems or needs related to the use of Debian
for bioinformatics, which I will detail in a slightly longer form here.
- When a project starts with a given version of a software, the researchers
are usually reluctant to upgrade, for good resons as scientific software does
not have a good record of maintaining stable APIs or outputs. This means
that projects end up trapped on a specific computer. Cloud computing could
propose a solution to this, maybe in line with the CUT concept, by taking
advantage of resources such as snapshot.debian.org to deliver reproducible
systems independantly on the state of the Debian archive. One could also
consider how to install multiple versions of a Debian package at the same time.
- Scientific software also tends to assume that it is run on computers with
unlimited memory and disk space, which is likely to cause problems on cloud
systems offering standard units that are often more limited. This calls for
parallelisation of the work, specific parametring of the cloud instances
(which typically have small or virtual temporary directories), scaling
and cost control, since cloud systems often bill in function of multiple
parameters such as up time, data transfer and disk activity.
- Given that the Summer of Code is about programming, what we need to build a
convincing project that a chance to get a slot is to find a clear target in
the issues above (or some that I would have forgotten), and propose a solution
that involves development (without reinventing the wheel) and improves Debian
in general, while solving important issues about doing bioinformatics in the
Cloud.
I hope this helps,
Have a nice day
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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