[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Re: Debian for Systems Biology

On Sat, 28 Jan 2006, Luca Brivio wrote:

Is there anybody interested to packaging software for systems biology?

<provocation mode>
Are you interested?
</provocation mode>

<honest mode>
Many people are, but have other things to do first.
</honest mode>

I'm a bioinformatics student, and I noticed nobody within Debian is
packaging systems biology-related tools (there is only an old ITP for

Wouldn't be useful to create a webpage like those
at http://www.debian.org/devel/debian-med/?

Well, 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.

Of course, actually systems biology inherit science more than medicine.
debian-science should have its own webpage, shouldn't it?

It should definitely but nobody has just done it.

A chaotic list with a few interesting tools for the main Debian
distribution with their licenses follows. Anyone could surely look

- Systems Biology Workbench (http://sbw.kgi.edu/research/sbwIntro.htm),
BSD license, contains Jarnac, JDesigner and a lot of other stuff.

- Dizzy (http://labs.systemsbiology.net/bolouri/software/Dizzy/),

- Bio-SPICE (https://biospice.org/visitor/index.php), which has its own
particular license (hope debian-legal helps!)

- PANTHER HMM library and tools (http://www.pantherdb.org/downloads/),
GPLed, concerning not only systems biology

-- without license and/or sourcecode (?):

- CellDesigner (http://www.celldesigner.org)?

- BioUML (http://www.biouml.org/) and some related things?

Thanks for your valuable list.  I guess it would be very helpful if you
would send a complete patch for the page


(including explicite license and short description) which would save
Tobias, our Debian-Med webmaster, some time.  It would even more speed
up things if you would try to build some packages that could be
sponsored by a DD to finally move the project in quastion to official

Thanks for your interesting input



Reply to: