Re: Presentation of Debian Med on local Next Generation Sequencing workshop (April)
Hi Steffen,
On Tue, 18 Mar 2014, "Steffen Möller" wrote:
> I was invited to a local (Northern Germany) workshop on next generation
> sequencing
> https://sites.google.com/site/nexgenseqmv/home/workshop
> to give a quick overview on what Debian/Ubuntu/BioLinux can do for them.
> This is a very friendly environment and besides
> * explaining how community-run Linux distros work
> * that Linux not necessarily means desktop,
> - but may mean virtual
> - or server and that
> - all major cloud services feature Debian images
Do not be shy here: by working "in Debian" we are pretty much automagically
benefiting from the work of more 'cloudy' people cooking up all the appliances
etc. Thus there is a huge benefit from sharing
expertise/responsibilities across different teams. That is why work of Debian
Med is automagically omni-present through-out all possible deployment scenarios
-- from cell phones (may be not by Debian itself, but by its derivative(s)), to
servers, clusters, "mainframe" architectures which might not even be generally
available (s390x, sparc) to regular mortals, and all possible clouds.
> * what Blends are
> * what packages are available for Next Generation Sequencing
> I am very eager to learn about what the audience expects from our distro(s).
I would also emphasize on unique "features" of Debian such as
- clear open standards (thus packaging is done "the right way" which
contributes to packages longevity)
- licensing "clearing house": helps with wider adoption and longevity
of software itself
- QA, such as build time testing: cannot be stressed enough on its
importance for anyone at least whispering about 'reproducibility'.
> Please kindly mention whatever issue is close to your heart that should
> be presented. I was very happy about the recent advent of the IGV.
> To have something tangible, I asked Roland from Qlustar.com to
> demonstrate over the coffee breaks how to set up a distributed work
> environment with Debian. Tony had found and introduced their
> technology for the Debian Med Sprint. He kindly agreed, so we will
> jointly learn about how NGS-savvy wet-lab biologists are approaching
> us.
heh -- never heard about qlustar... interesting to hear what you learn
from the coffee break
but also do not forget that Debian itself comes with many open HPC
related projects such as batch systems etc:
http://blends.debian.org/science/tasks/distributedcomputing
> Any suggestions on something fancy to display would be helpful.
Fancy... hm... I some times like to amuse "reproducibility-eager" folks
with commands such as
debootstrap --arch=i386 --include=python potato /tmp/potato http://archive.debian.org/debian
which in tandem with schroot could be used to bring Debian release from
decade(s) back with
novo(potato):~
$> python
Python 1.5.2 (#0, Dec 27 2000, 13:59:38) [GCC 2.95.2 20000220 (Debian GNU/Linux)] on linux2
Copyright 1991-1995 Stichting Mathematisch Centrum, Amsterdam
if you want to impress them even a bit more -- you could use apt-cacher-ng and
then debootstrap right there in matter of seconds (depending on your
harddrive/cpu speed) + pre-cooked schroot and you can really get them back into
the past ;) JUST MAKE SURE YOU HAVE ENOUGH DISK SPACE (do not ask why it is
in capitals)
> I would otherwise just dig into the data we are producing locally
> and show something.
So overall -- press not as much on flashiness (on-a-knee projects might be
flashier) but rather on long standing standards, quality, pervasiveness, shared
responsibility, impact.
if really bored, you can even watch my talk a year back, although I think
I have done much better ;-):
http://sea.ucar.edu/event/open-not-enough-benefits-debian-integrated-community-driven-computing-platform
My 1c ;)
--
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Senior Research Associate, Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
WWW: http://www.linkedin.com/in/yarik
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