This short presentation introduces Bioconductor. It outlines some of the challenges / opportunities facing the project, including cloud computing, python interoperability, and AI. A short section outlines my own work on data discovery using cellxgenedp and the ontology manipulation using OLSr.

I took a stab at trying to identify new (in the last release) relevant packages; this was not very successful because it was (a) difficult to winnow the new packages to relevant packages and (b) even more difficult to assess which packages were going to be important. For the later, it might be an interesting exercise to track the download statistics of each package as it ages; this data could be obtained from the (e.g., https://bioconductor.org/packages/release/bioc/VIEWS) file, and from package download statistics without too much difficulty.

One package catching my own attention was simona for semantic similarity in bio-ontologies, by Zuguang Gu. It imports (via a Java library) diverse ontology formats, computes many similarity metrics, and incldues visualization functions for both small and large ontologies. Definitely worth checking out further.

Writing the slides, I revisted the talk and short course material and slides produced for XM2023, the Brazilian Association for Bioinformatics and Computational Biology. I also revisited the one-page ‘cheat sheet’ for a 2-hour workshop / introduction from several years ago; the cheat sheet approach seems pretty interesting for this sort of short hands-on introduction.