Aw: Re: GSoC 2015 - should there be a Debian Med / Blend proposal separate from Debian?
Hi Andreas,
> Gesendet: Dienstag, 07. Oktober 2014 um 18:15 Uhr
> Von: "Andreas Tille" <andreas@an3as.eu>
> An: debian-med@lists.debian.org
> Betreff: Re: GSoC 2015 - should there be a Debian Med / Blend proposal separate from Debian?
>
> Hi Steffen,
>
> On Tue, Oct 07, 2014 at 05:13:06PM +0200, "Steffen Möller" wrote:
> > 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?
>
> I agree that there are several interesting points but I for myself
> regard the pure time spent into the mentoring itself as long enough. I
> do not want to spent it in the additional bureaucratic stuff. So I will
> not stop anybody with an honest attempt to do it but we probably need to
> be prepared to answer the question why a Debian subgroup wants to
> register as extra organisation. If I where in charge from the Google
> side of GSoC I would ask this question.
They should ask, indeed. I would not bother you with the admin but
would be unhappy if you would not mentor a project. Concerning the need
of a separation, well, this is deeply buried in my mailbox. I can say
so much that the "Gentle" project was proposed in 2010 IIRC and turned
down by the Debian GSoC admins at the time - even though it had passed
the threshold and found a student.
> Moreover your description of projects above IMHO fits to some extend
> to the general policy Debian has for GSoC.
This would be nice. Must have changed, then. The FPGA one would be a
prime candidate for the regular Debian GSoC, but this is more on FPGA
than on Debian and I had unfortunate experiences with such
non-Debian-centric projects in the past.
> BTW I would have expected something for Outreach Program for Women. I
> personally have put all my forces to make sure that all our packages are
> migrating to testing (Steffen, you remember that I asked for somebody
> else filing the needed ROM bug for mgltools-sff, right (hint, hint)) and
:) I do not . I'll look at it.
> so I was not really up for finding a proper project description. Any
> volunteer for this?
The student assigned for the Gentle project back then was female :)
Feel free to reuse that. I like the introductions to various topics the
OPW produced, maybe also the living tutorials is something that could
be addressed - I would just prefer to have myself concentrate on the
content parts of the mentoring for that, though.
If there are no other positive votes to run a DeibanMed-GSoC, then
this kills it, obviously :)
Many greetings
Steffen
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