Wed 17 December 2014
By C. Titus Brown
In science .
tags: python pyblosxom
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."
Anyway.
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.
--titus
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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