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Lisp(s) in Bioinformatics (Discussion)
Seth Carbon, (interested David Steinberg, Pjotr Prins), Bill Baumgartner
At many sites, the alpha and omega of languages just does not get much attention. It would be nice to touch bases with sites that actively use Lisp and see what is easy, what is hard, and what a modern Lisp stack for bioinformatics looks like.
Xena Browser allows one to send in scheme to a HTTP endpoint to perform queries. https://github.com/ucscXena
- Touch bases with other lispers about what they are doing
- Ask about what is going on in the Hunter Lab
While we were all unable to meet at the same time, I talked to all interested parties about their use and views of Lisps in their own work and where they might want to be with them in the future.
My personal takeaway from these talks is that there may be isolated use of lisps in "main" work, and these are often bridged over HTTP API interactions. Clojure also seems to enjoy slightly more day-to-day use in "main" work than other dialects. Similarly, ClojureScript seems to enjoy more adoption that other compile-down flavors (e.g. Parenscript) on web clients. While there has been some small resurgence of CLs generally, there does not seem to be much direct activity with them in practice within the people I spoke with. There seems to be a severe lack of non-proprietary triple/graph store software. An exceptional bright point in this seems to be the use of Guile in the Guix system/package distribution framework, which may help adoption elsewhere.
I feel that the takeaway for somebody looking to work with Lisp from this community would be to either look at ClojureScript in the client or Guile in the deep backend. For non-peripheral uses, islands can exist, but self-motivation may be necessary for non-peripheral use cases.