A review of "Tools and techniques for computational reproducibility"

Note: Last week, I submitted my review of Stephen R. Piccolo, Adam B. Lee, and Michael B. Frampton's paper, Tools and techniques for computational reproducibility. Soon after, Dan Katz wrote a blog post about notebooks, and in a comment I mentioned Piccolo's paper; and, after dropping a note to Dr. Piccolo, he put it up on bioRxiv! This, in turn, meant that I felt comfortable posting my review - since I sign my reviews, the authors already know who I am, so where's the harm? See below.

In this paper, Piccolo et al. do a nice (and I think comprehensive?) job of outlining six strategies for computational reproducibility. The point is well made that science is increasingly dependent on computational reproducibility (and that in theory we should be able to do computational reproducibility easily and well) and hence we should explore effective approaches that are actually being used.

I know of no other paper that covers this array of material, and this is a quite nice exposition that I would recommend to many. I can't evaluate how broadly it will appeal to a diverse audience but it seems very readable to me.

The following comments are offered as helpful suggestions, not criticisms -- make of them what you will.

The paper almost completely ignores HPC. I'm good with that, but it's a bit surprising (since many computational scientists seem to think that reproducible orchestration of many processors is an unachievable task). Noted in passing.

I was somewhat surprised by the lack of emphasis of version control systems. These are really critical in programming for ensuring reproducibility. I also found a missing citation! You should look at journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745 (yes, sorry, I'm on the paper).

Speaking of which, I appreciate the completeness of references (and even the citation of my blog post ;) but it would be interesting to see if Millman and Perez have anything to offer: http://www.jarrodmillman.com/oss-chapter.html. Certainly a good citation (I think you hit the book, but this is a particularly good chapter.)

I would suggest (in the section that mentions version control systems, ~line 170 of p9) recommending that authors "tag" specific versions for the publication, even if they later recommend using updated versions. (Too many people say "use this repo!" without specifying a revision.)

The section on literate programming could usefully mention that these literate programming environments do not offer good mechanisms for long running programs, so they may not be appropriate for things that take more than a few minutes to run.

Also, and perhaps most important, these literate programming environments provide REPL and can thus track exploratory data analysis and "harden" it when it works and the author moves onto another data analysis - so even if the authors don't want to clean up their notebook before publication, you can track exactly how they got their final results. I think this is important for practical reproducibility. I don't know quite what to suggest in the context of the paper but it seems like an important point to me.

Both the virtual machine and container sections should mention the challenges of raw data bundling, which is one of the major drawbacks here - not only is the VM large, but (unless you are partnering with e.g. Amazon to "scale out") you must distribute potentially large data sets. I think this is one of the biggest practical issues facing data intensive sciences. (There was a nice commentary recently by folk in human genomics begging the NIH to make human genomic data available via the cloud; I can track it down if the authors haven't seen it.)

I think it's important to emphasize how transparent most Dockerfiles are (and how this is a different culture than the VM deployment scene, where configuration systems are often not particularly emphasized except in the devops community). I view this as one of the most important cultural differences driving container adoption, and for once it's good for science!

The docker ecosystem also seems quite robust, which is important, I think.

[ ... specific typos etc omitted ... ]


C. Titus Brown, ctbrown@ucdavis.edu

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