Hello,
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-r
Hi Steffen,
On Tue, Mar 18, 2014 at 04:44:54PM +0100, "Steffen Möller" wrote:
> Hello,
>
> I was invited to a local (Northern Germany) workshop on next generation
> sequencing
> https://sites.google.com/site/nexgenseqmv/home/workshop
Hmmm, 15min is not much...
Well, all my presentations are o
Two additions:
You might also mention that we are training newcomers:
https://wiki.debian.org/DebianMed/MoM
On Tue, Mar 18, 2014 at 04:44:54PM +0100, "Steffen Möller" wrote:
> I was very happy about the recent advent of the IGV.
If you consider this package as important for your work - why d
Hi Steffen,
On Tue, Mar 18, 2014 at 10:04:34PM +0100, "Steffen Möller" wrote:
> > If you consider this package as important for your work - why didn't you
> > simply updated it?
>
> The main reason is that I did not expect it to be simple and days only
> have 24 hours.
Well, my days also have 24
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 fr
On Tue, Mar 18, 2014 at 10:12 PM, Yaroslav Halchenko
wrote:
> - QA, such as build time testing: cannot be stressed enough on its
> importance for anyone at least whispering about 'reproducibility'.
>
I would definitely prepare good material talking about
'reproducibility'. More below.
>> Any
On Wed, 19 Mar 2014, Carlos Borroto wrote:
> I lost some of my initial excitement about contributing to Debian Med.
> If I cannot use the results of my effort in the system where I
> actually do my job
quick side question: which are running ?
--
Yaroslav O. Halchenko, Ph.D.
http://neuro.de
On Wed, Mar 19, 2014 at 12:46:16PM -0400, Carlos Borroto wrote:
>
> I would definitely prepare good material talking about
> 'reproducibility'. More below.
I think the more effort we spent in autopkgtest suites the more we will
be able to come closer to reproducibility. I hope that this effort w
On Wednesday, March 19, 2014 23:09:25 Andreas Tille wrote:
> On Wed, Mar 19, 2014 at 12:46:16PM -0400, Carlos Borroto wrote:
> > I would definitely prepare good material talking about
> > 'reproducibility'. More below.
>
> I think the more effort we spent in autopkgtest suites the more we will
> b
On Wed, 19 Mar 2014, Diane Trout wrote:
> > I think the more effort we spent in autopkgtest suites the more we will
> > be able to come closer to reproducibility. I hope that this effort will
> > be rewarded by such projects who for whatever reason do not (yet) trust
> > our work.
> There's also
On Wednesday, March 19, 2014, Yaroslav Halchenko
wrote:
>
> On Wed, 19 Mar 2014, Carlos Borroto wrote:
>
> > I lost some of my initial excitement about contributing to Debian Med.
> > If I cannot use the results of my effort in the system where I
> > actually do my job
>
> quick side question: wh
On Wed, 19 Mar 2014, Carlos Borroto wrote:
> > I lost some of my initial excitement about contributing to Debian Med.
> > If I cannot use the results of my effort in the system where I
> > actually do my job
> quick side question: which are running ?
>Are you asking a
On Wed, 19 Mar 2014, Diane Trout wrote:
> > I think the more effort we spent in autopkgtest suites the more we will
> > be able to come closer to reproducibility. I hope that this effort will
> > be rewarded by such projects who for whatever reason do not (yet) trust
> > our work.
> There's also
On Wed, Mar 19, 2014 at 08:31:06PM -0400, Carlos Borroto wrote:
> BioLinux, from where CloudBioLinux comes, is a close, but
> my experience is that the collaboration is not as close as you would
> expected.
>From my perspective the collaboration between Debian Med and BioLinux is
as close as the t
On Thu, Mar 20, 2014 at 01:12:27PM +0100, "Steffen Möller" wrote:
>
> Brainstorming here: we'd need a platform to promote community contributions
> to scientific Open Source software. Something tells me, that this could
> be something like "us" (whatever "us" is), but in some less distribution
> c
Le Wed, Mar 19, 2014 at 10:20:33PM -0400, Yaroslav Halchenko a écrit :
>
> upon brief look: I have apt-get sourced cufflinks -- found no
> unittests available
>
> the same for tophat
Hi Yaroslav,
yes, unit tests are not always available, but I see more and more editorials in
top journals advoca
On Fri, 21 Mar 2014, Charles Plessy wrote:
> For packages without upstream tests, in the meantime, even the most simple
> tests like running the command with the --help option, are potentially useful.
+10 ;) I also try to run some Demo or Example script if such is
provided (often via xvfb) to in
> Gesendet: Dienstag, 18. März 2014 um 17:11 Uhr
> Von: "Andreas Tille"
> An: debian-med@lists.debian.org
> Betreff: Re: Presentation of Debian Med on local Next Generation Sequencing
> workshop (April)
>
> Two additions:
>
> You might also m
Hello,
> >Beside the two big ones I already mentioned, Galaxy and CloudBioLinux, I
> >don't know any other good example of a popular system for computational
> >biology not using official packages. I also don't know of an example of a
> >system that does. BioLinux, from where Cloud
Hello,
it all went well, I tend to think. To mention something
soon-to-be tangible, the authors of
http://bioinf.uni-greifswald.de/augustus/
attended and are now making up their minds and code
to separate their algorithm properly from their data (huge).
Otherwise, Roland and I had tons of talks
> Brainstorming here: we'd need a platform to promote community contributions
> to scientific Open Source software. Something tells me, that this could
> be something like "us" (whatever "us" is), but in some less distribution
> centric way. For Bioinformatics, the Open Bioinformatics Foundation c
On Thu, Mar 20, 2014 at 12:02:46PM -0700, Diane Trout wrote:
> Also the IPython developers are really interested in trying to create
> "executable papers" https://plus.google.com/+FernandoPerez/posts/gwxhuwgJRED
Which is, eventuelly, Donald Knuth's idea.
Karsten
--
GPG key ID E4071346 @ gpg-ke
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