Summary of existing programs, their licences, and their potential to be integrated in Debian
In the following pages, we are currently building a list of programs of interest for a yet to create ?DebianBiology custom distribution (or to enhance DebianMed if it makes more sense). Included in the list are very popular programs which, because of their licence would not be able to be officially packaged in main and/or non-free.
The final goal is to have useful toolchains made from free packages, that is, in main.
DebianBioinformatics (workflow, collaborative, general purpose tools)
DebianBioinformaticsLibraries (libraries for writing bioinformatics software)
DebianBiophysics (tools for molecular docking, molecular dynamics, ...)
DebianGenetics (tools for genotyping, haplotyping, and linkage analysis)
DebianGenomics (tools for analysing whole genomes)
DebianMicroscopy (tools for image/video analysis)
DebianMolecularBiology (for instance plasmid drawing programs)
DebianProteomics (tools for analysing whole proteome)
DebianSequenceAnalysis (tools to manipulate and analyse sequences)
SequenceAlignment (Many multiple sequence alignment programs were recently packaged)
DebianSystemsBiology (tools to for data integration, mining and modeling)
Having some wrappers to manage databases whose content is free would be nice, too.
The following area are now well covered in Debian.
SequenceAlignment (multiple sequence alignment. Pairwise alignment will be a separate effort).
Most programs which are already packaged are installed by the following metapackages:
Biology tools that could be considered for inclusion in Debian
- Molecular Biology and Molecular Genetics
- Systems Biology:
Packaging efforts in other distributions