GSoC 2015 - should there be a Debian Med / Blend proposal separate from Debian?
Hello,
The projects of Debian for the Google Summer of Code
http://www.google-melange.com/gsoc/homepage/google/gsoc2015
have their focus on the Debian infrastructure. It was quite some earning
experience for me, but eventually I have grasped that this was a good thing.
However, my personal ambition for Debian comes for a good part from the
practical side of it all - it is my Bioinformatics desktop and/or server - and
I want that helped by a GSoC, too.
Now Debian is good (best?) with sharing libraries between otherwise
independent software packages, but we are yet doing little to help
with the inter-operability of those packages. And beyond our Wiki there
is nothing that informs others about how to address our daily routine.
This GSoC could help Debian (as a whole, not just "Med") to strengthen
its ties with upstream and foster developments to help with the
interaction of tools and the promotion of such workflows.
While I see naturally quite some opportunities in Bioinformatics, I
am highly interested to see our other blends address such workflows,
too. So this could be a Debian Blend Project. Here some ideas:
* Get Gentle (molecular cloning) dissected into several interoperating
small command line tools and combine it with a workflow environment
The reason for that is that molecular cloning is an iterative process
and Gentle (like all other tools for molecular cloning I looked at,
correct me if I am wrong) are dysfunctional with a representation of
the steps taken to yield a particular amplicon. The workflow is the
recipe to pass to the technical assistant. The workflow engine could
be Taverna as a start, which is offered as a Debian package by upstream
and ... well ... some day my package for it will work, there may be
others.
* Functional Tutorials
We started to look at Youtube to learn about how to use any particular
software. This hurts. Just a bit. I would very much like to see something
in the lines of how Docker or VIM introduces itself as a template for
biological sequence analysis.
* Unit Tests
Andreas has already been much at it. There should be more. And more.
This GSoC could help. I reckon that we could also come up with new ideas
about what such tests could work like, for instance when there is
no perfect answer to a problem, as in the assembly of complete genomes
from short sequences.
* FPGA for application acceleration
It was amazing to see how quickly the BitCoin folks jumped from GPUs
to FPGA to ASICs. There is quite a number of affordable FPGA boards
now available that would be good to have closer to our distribution
to prepare for application acceleration. This fancy Open Source Laptop
https://www.crowdsupply.com/kosagi/novena-open-laptop
even has an FPGA within - albeit quite a small one. I would very
much like to see something happening to help sharing Open Source
hardware descriptions between such devices.
...
There is more. Much more. But how is your feeling about it all? Is it a
good idea to have this organised in parallel to what the core of Debian
is doing? Are such worthwhile projects in the first place? Are there
other GSoC organisations that are likely to care for them?
Best,
Steffen
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