PlateWash

Julia could be a big win, not just b/c of the notation, but the dependency control is a first-class language feature. Also, the Lispy-ness of Julia allows to do things like Latexify expressions. To quote someone upthread: https://news.ycombinator.com/item?id=24260590 > Everyone just put together a few text files and Python or MATLAB scripts that output some numbers that went into Excel or gnuplot scripts that got copy-pasted into LaTeX documents with suffixes like "v2_final_modified.tex", shared over Dropbox. It would be amazing to have an environment that could handle the entire workflow. Not everybody has time to make an executable thesis like this person did: https://github.com/4kbt/PlateWash

I heartily disagree -- reproducible analysis is essential for the intercomparison of analyses between specialist research groups. Here is my thesis work, minus the data, which is too large to store within a GitHub repo. By calling `make`, it goes from raw data to final document in a single shot. The entire workflow, warts and all, can be audited. If you see a bug or concern, please let me know: https://github.com/4kbt/PlateWash

I don't do it well. See https://github.com/4kbt/ReplicableAnalysis and https://github.com/4kbt/PlateWash as examples. The former is smaller/less complicated. The latter was my thesis work -- more complicated and (unfortunately) abuses recursive calls to Make.

I'd go as far as to argue that such a plan is essential to reproducibility (and it makes your work faster and less error-prone). My take on the same plan ( "make thesis" ): It's not pretty, but it works. https://github.com/4kbt/PlateWash Unblinding tweet: https://twitter.com/CharlieHagedorn/status/59565285891105177... Finished product: https://digital.lib.washington.edu/researchworks/handle/1773...

It was my first independent Monte Carlo calculation -- changed my life. That project led directly to the 'rand' call in this function [1] 13 years later and fundamentally altered the way I think about data analysis. [1] https://github.com/4kbt/PlateWash/blob/master/mlib/bootstrap...