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Last active August 22, 2019 10:08
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Resources for documenting and publishing code with biological science
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some_resources.md

It seems you are asking about a few related things here. There is no short answer as some of this depends on your motivation, time, resources, skills, target audience, journal, etc. Plus a lot of the best practices are subjective or in flux.

I'd suggest looking at some of the resources below, find some direction and examples you find admirable, and see what you'd like to implement for this time. And what is possible for next time. Someone suggested using Jupyter notebooks which is great especially since you can now share live ones using Binder, see https://github.com/fomightez/methods_in_yeast_genetics/tree/master/cell_density_estimator for an example. Alternatively or as a companion site/documentation, I suggest using read the docs (https://readthedocs.org/) and Github for a making a step by step version that a biologist with limited computational skills could use it (or youself maybe a year from now) and then you can adapt that into a paper. That way you have a long version that the paper can refer readers to within manuscript. By the way, I think most things can be done at Github by editing right in the browser and so don't be put off by thinking you need to learn git.

I wish I had more publication examples to include but I don't have a good list right now. (I may try to update this eventually.)

Several resources in no particular order that may help you get started:

Example publications

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