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How to read this spreadsheet
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Rows describe software that should make it into the Debian distribution. Different topics are separated into different tabs. "Virus" is meant to harbor all that is likely relevant for COVID-19 research. No exact threshold set.
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Columns are mostly self-explanatory. The first columns describe the software, later columns describe their association with a particular workflow. Every workflow is expected to have a package that implements it.
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Color coding
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greenall fine
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yellow
something stuck in salsa
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redmissing
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bluewe shall not care
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Different shades of these main colors are used in different columns. That is mostly for historical reasons. Later columns use the colors that are more easily accessible in the color palette.
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The "yes" for the conda packages at times is not informative enough to find the package. Later additions specify the conda channel (conda-forge, qiime2, bioconda) to non-ambiguously specify a package.
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The "yes" for the Debian package at times does not suffice to identify the package. The Debian package name is then given. The hyperlink behind the "yes" or the package name shall point to the salsa repository. Some entries point to tracker.d.o - both is fine.
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When the Debian package name and the upstream name diverge, the first column typically holds the Debian package name and the second column the upstream name. But not all tabs do it this way.
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The link from a Debian package to a workflow is typically by "Includes". For a few packages it is "post-processing", which basically extends the workflow. This shall evolve.
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For write permissions to this spreadsheet please say hello on the Debian Med mailing list.
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Tabs
Intent: gather all software that likely contributes to the
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Biological
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Virus
research of SARS-CoV-2 induced phenotypes - this tab triggered it all
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Immunoinformatics
software that helps interpreting our immune system
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Microbiome
interpretation of relative abundancies of bacteria and yeasts in our gut and elsewhere
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Molecular Tumor Board
clinical interpretation of all evidence gathered on a patient
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Biotechnical
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Nanopore
interpretation of data generated with that disturbing new sequencing technology
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bulk RNA-seq
what was once called "next-generation sequencing" is now how everyone is doing it
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single-cell RNA-seq
yes, it is now possible to determine how cells differ within a tissue
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Genome structure
determination where nucleotide variants are, how the genome is assembled, detection of fusions/deletions/copy-number-variations, modifications
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3D docking
link to cheminformatics - find drugs, suggest why mutations have an effect
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Synthetic Biology
yes, this exists, also in software, and we are not yet doing enough to cover this in Debian - after the pandemic
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Technical
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Java
organisation of our community to address Java issues
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Data
organisation of what is not software
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Education
avoidance of an echo chamber - we need to get out into the world
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Other
differentiation of this sheet - there is no progress without "other"
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If you feel like helping out but are not really sure about where to start, the mailing list should find someone to mentor you.
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