Re: Debian for Systems Biology
On Sun, Jan 29, 2006 at 06:14:42PM +0100, Andreas Tille wrote :
Hi Andreas,
I will answer to all your mails in one, in order to limit the traffic.
> >Why not use the already-existing Debian wiki page at
> >http://wiki.debian.org/DebianScienceBiology ? (For those who aren't
> >aware, you don't need to be a Debian Developer to edit the wiki; you
> >just need to create an account there for yourself.)
>
> Ahh, this is also a reasonable idea: We could just use this wiki as
> kind of a TODO-list for updates of
>
> http://www.debian.org/devel/debian-med/microbio
Do not worry for this. This page makes sense, and is very useful for
finding third party packages. Also I am the translator for its french
version, so I will definitely not waste Tobias work, nor my work. The
only critisism I have on it is its name: I guess that it contains
molecular biology software because it started with gene discovery on
microbial genomes, ans I think that when seeing the URL, a lot of
persons will think that it is related to medical bacteriology, and wil
overlook it. On the other hand, on the main page, the link name is
molecular biology, which makes more sense. So if you modify the
debian-med structure one day, I think it would be worthwile try to solve
this, but I suppose that changing the name now would break links and
make this page lose readers instead of winning some.
> So if a biologist installs a imaginary meta package 'bio-genetics' it
> might perfectly be possible that a user working in medical care
> installs the 'med-bio' package (which just exists!) and gets nearly
> the same set of packages on his box.
Thanks for the link (http://people.debian.org/~tille/cdd/). I guess I
have to read it before answering. Anyway, I think that most of the work
is not the meta-packaging, but to gather the software into debian. Also,
I wonder how some existing packages could be tweaked. For instance, the
search box of firefox can be used to query very relevant databases,
such as pubmed.gov or genbank (http://www.ncbi.nlm.nih.gov/Genbank/),
and shipping this configuration by default would make senes on a CDD.
Figuring out how to do this is definitely one of my goals.
> Currently Debian-Med cares for biological stuff because many
> biological tools are just used in medical care and nobody else cared
> for biological software explicitely.
So I will subscribe to the debian-med list to avoid duplication of the
work.
Best,
--
Charles
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