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The Debian Med project prepares packages that are associated with medicine, pre-clinical research, and life sciences. Its developments are mostly focused on three areas for the moment: medical practice, imaging and bioinformatics.
Over the years, several initiatives have spawned that address software provision in the scientific disciplines like chemistry or bioinformatics. Debian Med is not a competitor to these efforts but a nucleus for developers and a platform to enable that development. The ultimate goal of our packaging work is to make Debian, and therefore derivatives including Ubuntu, the best possible platforms for medical and life sciences research. As the packages are prepared to Debian policy standards and contributed to the regular Debian and Ubuntu repositories, the Debian Med project is classified as a Debian Pure Blend.
To commit changes, join the webwml project on Alioth
Relevant Alioth projects:
Information for end users: is collected in the FAQ
Email contact: <firstname.lastname@example.org>
We are proud of: existing and prospective packages
See our activities realtime on: Debian Med developer page
Bugs of Debian Med relevant packages: http://debian-med.alioth.debian.org/bugs
Relevant Ubuntu projects:
Contributing to Debian Med
From the developer to the user, there is a long chain of tasks in which we always welcome participation. First we must keep ourselves informed about the software landscape in biology and medicine. Software to be packaged is chosen according to criteria such as users' need and the consistency of the distribution. Once in Debian, the software is monitored for its quality and bugs are fixed, if possible in collaboration with the upstream maintainer(s). All this work would not be very useful if it remains confidential. We also dedicate some time to advertise it to the world via http://www.debian.org and to ease the integration of new members through this wiki.
Please contact us on email@example.com if you want to help to make medical and biological software available to Debian users. Next steps are described very verbosely in our team policy document which describes the workflow in our team and should guide you step by step into the rules we have agreed upon.
If you speak a language other than English, you can contribute rightaway with translations of package descriptions at the Debian Description Translation Project. When working on these, you will find immediate targets for improvements of the original English versions, too. For these, though, you need access to Debian Med's source code repository. Very welcome are tutorials that guide Debian users towards the use of packages to their immediate benefit. You may also consider to write respective articles for Magazines, be they online or in print.
There is a list of active Debian Med developers including data about motivation and activity in the project.
If you would like to contribute to Debian Med you might also have a look at DebianMedTodo that contains a list of tasks to do.
If you are a newcomer and have no idea how to contribute you might like to join the Mentoring of the Month effort.
Services for developers
Progress report on svn repository
A specific page is available for non-free packages
Mailing lists and IRC
IRC: #debian-med on irc.debian.org (OFTC)
getData - automating routine work for the download and update of public databases
Using Subversion and Git to group-maintain packages
Our source packages are managed in Subversion and Git repositories. Every Debian Developer and member of the Alioth debian-med project have write permissions on them.
When using Debian or Ubuntu for your work, you may find it appropriate to cite any of the following publications:
S. Möller, H. N. Krabbenhöft, A. Tille, D. Paleino, A. Williams, K. Wolstencroft, C. Goble, R. Holland, D. Belhachemi, C. Plessy (2010) "Community-driven computational biology with Debian Linux" BMC Bioinformatics, 11(Suppl 12):S5
A. Tille, S. Möller, M. Hanke, Y. Halchenko (2011) "Debian Med - Integrated software environment for all medical purposes based on Debian GNU/Linux", Med@Tel 2011
BOINC, the Debian packages for the Berkeley Open Infrastructure for Network Computing, fosters the active involvement in biomedical research for everybody by merely contributing CPU time.
rosetta molecular modeling tool
DebianMedProspective: study of other workflows to solve the growth crisis that we will soon or later face.
- Supported Open Access Journals
- News sites
- Similar Initiatives
BioPuppy - Debian Med packages are transformed to a Puppy-based LiveCD
Bio-Linux .deb packages
GoeBix Bioinformatics LiveDVD from Göttingen (existing)
BOSC Live CD (planned)
- Categorization and evaluation of medical software