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Community-driven computational biology with Debian Linux.

Steffen Möller1, Hajo Nils Krabbenhöft, Andreas Tille

  • 1University Clinics of Schleswig-Holstein, Department of Dermatology, formerly University of Lübeck, Institute for Neuro- andBioinformatics, Ratzeburger Allee 160, 23530 Lübeck, Germany. moeller@debian.org

BMC Bioinformatics
|January 8, 2011
PubMed
Summary
This summary is machine-generated.

The Debian Med initiative offers integrated software packages for bioinformatics research, simplifying tool access and ensuring consistent research conditions for distributed teams. This promotes global collaboration in computational biology.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Medical Informatics

Background:

  • Open Source software is vital for bioinformatics research, offering free tools and resources.
  • A robust infrastructure is needed to share and update these tools for diverse computing environments.

Purpose of the Study:

  • To present the Debian Med initiative as a solution for packaging and distributing bioinformatics software.
  • To facilitate the use of these packages in research workflows and cloud environments.

Main Methods:

  • Debian Med provides ready-to-use, coherent software packages.
  • Packages are integrated with Taverna workflows using the UseCase plugin for execution management.
  • The initiative supports deployment in cloud computing environments.

Main Results:

  • Debian Med offers accessible and consistent software packages for medical informatics and bioinformatics.
  • These packages enable streamlined execution in Taverna workflows on various machines.
  • Availability in cloud environments allows sharing of hardware and analysis pipelines.

Conclusions:

  • Debian Med bridges the gap between software developers and users.
  • It simplifies the distribution of new software and data releases for computational biology.
  • Ensures consistent tool versions for geographically distributed research teams, enhancing global collaboration.