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I'm Viola (28) from Maubeuge, France. <<BR>><<BR>>
I'm learning Hindi literature at a local high school and I'm just about to graduate.<<BR>><<BR>>
I have a part time job in a backery.<<BR>><<BR>>
<<BR>><<BR>>
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{{http://people.debian.org/~tille/debian-med/logos/med-06.jpg}}

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
[[http://www.debian.org/doc/debian-policy|Debian policy standards]] and
contributed to the regular [[http://packages.debian.org|Debian]] and
[[http://packages.ubuntu.com|Ubuntu]] repositories, the Debian Med
project is classified as a [[DebianPureBlends|Debian Pure Blend]].


 * '''Website''': ''http://www.debian.org/devel/debian-med/''
  * ''To commit changes, join the [[https://alioth.debian.org/projects/webwml/|webwml]] project on Alioth''
 * '''Relevant Alioth projects''':
  * ''http://alioth.debian.org/projects/debian-med''
    * Group policy: http://debian-med.alioth.debian.org/docs/policy.html
  * ''http://alioth.debian.org/projects/blends''
 * '''Information for end users''': ''[[DebianMed/HowToGet|is collected in the FAQ]]''
 * '''Email contact''': ''<<MailTo(debian-med@lists.debian.org)>>''
 * '''We are proud of''': ''[[http://debian-med.alioth.debian.org/tasks|existing and prospective packages]]''
 * '''See our activities realtime on''': ''[[http://debian-med.alioth.debian.org/|Debian Med developer page]]''
 * '''Bugs of Debian Med relevant packages''': ''http://debian-med.alioth.debian.org/bugs''
 * '''Relevant Ubuntu projects''':
  * '''Unofficial packages for Ubuntu''': ''https://launchpad.net/~debian-med/+archive/ppa''
  * '''Launchpad team''': ''https://launchpad.net/~debian-med''
== 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 debian-med@lists.debian.org if you want to help to make medical and biological software available to Debian users. Next steps are described very verbosely in our [[http://debian-med.alioth.debian.org/docs/policy.html|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 [[https://www.debian.org/international/l10n/ddtp|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 [[DebianMed/Developers|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 [[DebianMed/MoM|Mentoring of the Month]] effort.


== Services for developers ==

=== Web sites ===
  * a [[http://alioth.debian.org/projects/debian-med/|Debian Med Alioth project]] which controls the access to a subversion (svn) repository at svn://svn.debian.org/svn/debian-med/ ([[http://svn.debian.org/wsvn/debian-med|web svn]])
  * [[http://debian-med.alioth.debian.org|Progress report]] on svn repository
  * A specific page is available for [[DebianScienceSampleLetter|non-free packages]]

=== Mailing lists and IRC ===
  * [[http://lists.debian.org/debian-med/|Debian Med]] - general discussion list ([[http://lists.debian.org/debian-med/|Archives]])
  * [[http://lists.alioth.debian.org/mailman/listinfo/debian-med-packaging|debian-med-packaging]] - reports and discussions on packages ([[http://lists.alioth.debian.org/pipermail/debian-med-packaging/|Archives]])
  * [[http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit|debian-med-commit]] - reports on commits to svn repository ([[http://lists.alioth.debian.org/pipermail/debian-med-commit/|Archives]])

  * The persons who know the administrative password of the Alioth mailing lists are AndreasTille, CharlesPlessy and NelsonOliveira.
 * IRC: [[irc://irc.debian.org/debian-med|#debian-med]] on irc.debian.org (OFTC)

=== Community projects ===

   * [[getData]] - automating routine work for the download and update of public databases
   * [[DebianMed/LiveCD]] - preparing [[DebianMed|Debian Med]] for clouds and your USB stick

=== Meetings ===
  * [[CustomDebian/Extremadura2007]]
  * [[DebianMed/Meeting/Luebeck2011|First Sprint]]
  * [[DebianMed/Meeting/Southport2012|Second sprint]]
  * [[DebianMed/Meeting/Kiel2013|Third sprint]]
  * [[DebianMed/Meeting/Aberdeen2014|Fourth sprint]]

=== 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.

Our [[http://debian-med.alioth.debian.org/docs/policy.html|Group policy]] explains most
details. The [[http://debian-med.alioth.debian.org/docs/policy.html#ssh-tips|SSH]],
[[http://debian-med.alioth.debian.org/docs/policy.html#subversion-tips|Subversion]]
and [[http://debian-med.alioth.debian.org/docs/policy.html#git-tips|Git]]
tips are a recommended reading for the beginners.

== References ==

When using Debian or Ubuntu for your work, you may find it appropriate to cite any of the following publications:

 1. S. Möller, H. N. Krabbenhöft, A. Tille, D. Paleino, A. Williams, K. Wolstencroft, C. Goble, R. Holland, D. Belhachemi, C. Plessy (2010) "[[http://www.biomedcentral.com/1471-2105/11/S12/S5|Community-driven computational biology with Debian Linux]]" BMC Bioinformatics, 11(Suppl 12):S5
 1. A. Tille, S. Möller, M. Hanke, Y. Halchenko (2011) "[[http://people.debian.org/~tille/talks/201104_luxembourg/paper/debian-med.pdf|Debian Med - Integrated software environment for all medical purposes based on Debian GNU/Linux]]", [[http://www.medetel.lu/index.php?rub=proceedings&page=info|Med@Tel 2011]]


== Related pages ==
 * [[http://www.debian.org/devel/debian-med/|Debian Med home page]]
 * DebianMedBio
  * [[pkg-bioc]], The packaging effort for the !BioConductor R libraries
  * [[pkg-escience]], Effort to provide packages for controlling web services in bioinformatics
 * DebianMedImaging
 * [[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.
 * [[debichem]], applications for chemistry ([[http://debichem.alioth.debian.org/|Alioth]])
 * [[http://en.wikipedia.org/wiki/List_of_open_source_healthcare_software|Quite complete list of medical software in Wikipedia]]
 * [[rosetta]] molecular modeling tool
== See also ==
 * The work of the Debian Med packaging team in [[http://qa.debian.org/developer.php?login=debian-med-packaging@lists.alioth.debian.org|Debian]] and [[https://launchpad.net/~debian-med-packaging/+packages|Ubuntu]].
 * [[DebianMed/Developers]].
 * DebianMedProspective: study of other workflows to solve the growth crisis that we will soon or later face.
 * Supported Open Access Journals
  * Genome Biology
  * [[http://compbiol.plosjournals.org/|PLoS Computational Biology]]
  * [[http://bioinformatics.oxfordjournals.org/|Bioinformatics]] (OUP)
  * [[http://www.biomedcentral.com/bmcbioinformatics/|BMC Bioinformatics]]
  * [[http://www.scfbm.org/|Source Code for Biology and Medicine]]
  * [[http://www.bioinfo.de/isb/|In Silico Biology]] (International Fully Free online+print Journal, most in sync with Debian's principles)
 * News sites
  * [[http://www.linuxmednews.com/|LinuxMedNews]]
 * Similar Initiatives
  * [[http://www.biopuppy.org|BioPuppy]] - Debian Med packages are transformed to a Puppy-based LiveCD
  * [[http://nebc.nerc.ac.uk/biolinux.html|Bio-Linux]] .deb packages
  * [[http://bioinf.nuigalway.ie/bioconductorbuntu.html|BioconductorBuntu]]
  * [[http://www.bioinf.med.uni-goettingen.de/teaching/goebixdvd/|GoeBix]] Bioinformatics LiveDVD from Göttingen (existing)
  * [[http://open-bio.org/wiki/BOSC/liveCD|BOSC Live CD]] (planned)
  * [[http://www.randomfactory.com/lfb/lfb.html|The Linux for Biotechnology cdrom project]] (RPMs)
  * [[http://fedoraproject.org/wiki/SIGs/FedoraMedical|FedoraMedical]]
  * [[http://en.opensuse.org/OpenSUSE-Medical|OpenSUSE-Medical]]
  * [[http://www.wurlug.org/wurlug/index.php/BioNode|BioNode]], a flavor of [[https://github.com/chapmanb/cloudbiolinux|CloudBioLinux]] (virtual machine build system)
 * Categorization and evaluation of medical software
  * [[http://www.medfloss.org/node/62|medfloss.org]]

http://people.debian.org/~tille/debian-med/logos/med-06.jpg

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.

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 debian-med@lists.debian.org 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

Web sites

Mailing lists and IRC

Community projects

Meetings

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.

Our Group policy explains most details. The SSH, Subversion and Git tips are a recommended reading for the beginners.

References

When using Debian or Ubuntu for your work, you may find it appropriate to cite any of the following publications:

  1. 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

  2. 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

See also