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Showing posts from May, 2019

Where's the code?

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Yesterday I posted this tweet, which seemed to resonate with quite a few people.  Ok, at least it got more likes than my tweets usually do. Of course, while writing snarky tweets is fun, it doesn’t do anything to address the underlying problem. Computational Chemistry and Cheminformatics (including applications of machine learning in drug discovery) are a few of the only remaining fields where publishing computational methods without source code is still deemed acceptable.  I spend a lot of time reading the literature and am constantly frustrated by how difficult it is to reproduce published work.Given the ready availability of repositories for code and data, as well as tools like Jupyter notebooks that make it easy to share computational workflows, this shouldn’t be the case.  I really liked this tweet from Egon Willinghagen, one of the editors of TheJournal of Cheminformatics (J. ChemInf.).

Shouldn’t we be able to download the code and data used to generate a paper and quickly repro…