diff options
Diffstat (limited to 'website/content/en/status/report-2022-10-2022-12/biology.adoc')
| -rw-r--r-- | website/content/en/status/report-2022-10-2022-12/biology.adoc | 28 |
1 files changed, 28 insertions, 0 deletions
diff --git a/website/content/en/status/report-2022-10-2022-12/biology.adoc b/website/content/en/status/report-2022-10-2022-12/biology.adoc new file mode 100644 index 0000000000..6e685ef73b --- /dev/null +++ b/website/content/en/status/report-2022-10-2022-12/biology.adoc @@ -0,0 +1,28 @@ +=== Another milestone for biology ports + +Links: + +link:https://github.com/auerlab/biolibc-tools[Biolibc-tools] URL: link:https://github.com/auerlab/biolibc-tools[https://github.com/auerlab/biolibc-tools] + +link:https://github.com/auerlab/fasda[Fast And Simple Differential Analysis] URL: link:https://github.com/auerlab/fasda[https://github.com/auerlab/fasda] + +Contact: Jason Bacon <jwb@FreeBSD.org> + +The biology category in ports continues to grow and mature, and reached another milestone in 2022q4 with the introduction of the rna-seq metaport. + +The fields of genomics, and more generally, bioinformatics, are often referred to as the "wild west" of computational science. +Analyses are typically mired by a lack of clear documentation, and difficulties deploying and using software. +Many scientific software developers do not understand the potential of package managers to simplify their lives and the lives of their users. +As a result, much scientific software is deployed using ad hoc "caveman" installations involving overly complicated and unreliable build systems that either bundle dependencies or attempt to work with random installations thereof. + +Work has been ongoing to make FreeBSD ports a model of how easy scientific software deployment should be. +It now contains a solid core of many of the most commonly used open source applications in biological research. + +This quarter saw the completion of a tool chain for one of the most important types of analysis, known as RNA-Seq. +RNA-Seq measures the abundance of RNA, and hence gene activity, in tissue samples. +All of the tools needed to perform a typical RNA-Seq analysis can now be installed on FreeBSD using: + +`pkg install rna-seq` + +This includes many mature existing tools as well as new tools developed on FreeBSD, such as FASDA and biolibc-tools, easy-to-use replacements for some of the more troublesome tools traditionally used in an RNA-Seq pipeline. + +Software deployments for RNA-Seq that traditionally have taken weeks or longer can now be performed on FreeBSD in a few minutes with a single command. +Scientists can spend their time doing science rather than struggling with IT issues. |