amoghpj / emacs-for-biologists Goto Github PK

Thanks Amogh for creating the repo.

If we're going for the style like awesome-cl (which is great), I'm pretty sure this repo will be useful for biologists who know Emacs well enough.

But if we also want to attract perspective users - by showing that how the tools in the repo might be useful in their research - perhaps we'll need more than a list of repos, but also example gifs/vids? This might be useful for both new comers and power users?

A biorxiv interface similar to the arxiv mode package will be nice to have.
I took a cursary look at the biorxiv API, and maybe I didn't find the right page, but it looks very limited.

Desired features, if a stable API exists:

1. Search preprints by key word
2. Interface to display title, authors, upload dates
3. Utilities to download PDFs, bibtex citations, and DOIs.
4. Optional, have some way of getting the publication status for local files managed by biorxiv mode. (If a preprint is published, mark that entry with a star or something.)

I have been playing around with primer3, blast, and CRISPR guide design tools like CCTop. I have a functioning python workflow to design primers and guides for gene deletions. Is it worth systematizing this to create an interface in emacs?
The main issues that I need to think about are:

1. Visualizing annotations, say from genbank files. Is there a plain text visualizer for genbank files?
2. Interface to highlight a sequence region of interest and perform an action on it, say design primers.
3. Interfacing emacs with standalone tools. Bioconda does a good job of installing binaries, and I don't want to lose that power. But bundling external dependencies with an elisp wrapper seems painful. I'll need to see how other "wrapper" tools do this in emacs.