The post-apocalyptic world of binary containers

Written by: C. Titus Brown

Primary Source: Living in an Ivory Basement

The apocalypse is nigh. Soon, binary executables and containers in object stores will join the many Web-based pipelines and the several virtual machine images on the dystopic wasteland of “reproducible science.”


I had a conversation a few weeks back with a senior colleague about container-based approaches (like Docker) wherein they advocated the shipping around of executable binary blobs with APIs. I pointed out that blobs of executable code were not a good replacement for understanding or a path to progress (see my blog post on that) and they vehemently disagreed, saying that they felt it was an irrelevant point to the progress of science.

That made me sad.

One of the things I really like about Docker is that the community emphasizes devops-style clean installs and configurations over deployment and distribution of binary blobs (images, VMs, etc.) Let’s make sure to keep that; I think it’s important for scientific progress to be able to remix software.

I’ll just close with this comment:

The issue of whether I can use your algorithm is largely orthogonal to the issue of whether I can understand your algorithm. The former is engineering progress; the latter is scientific progress.


p.s. While I do like to pick on the Shock/Awe/MG-RAST folk because their pipeline is utterly un-reusable by anyone, anywhere, ever, I am being extremely unfair in linking to their paper as part of this blog post. They’re doing something neat that I am afraid will ultimately lead in bad directions, but they’re not espousing a binary-only view of the world at all. I’m just being funny. Honest.

p.p.s. Bill Howe and I also agree. So I’m being multiply unfair. I know.

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C. Titus Brown
C. Titus Brown is an assistant professor in the Department of Computer Science and Engineering and the Department of Microbiology and Molecular Genetics. He earned his PhD ('06) in developmental molecular biology from the California Institute of Technology. Brown is director of the laboratory for Genomics, Evolution, and Development (GED) at Michigan State University. He is a member of the Python Software Foundation and an active contributor to the open source software community. His research interests include computational biology, bioinformatics, open source software development, and software engineering.