(Some) Principles of Computational Science

I'm just finishing up my Computational Science for Evolutionary Biologists course, and I'm finding it tricky to come up with a good high-level summary of what I would like them to take away. As you can see from the class notes they've done some reasonably neat stuff with Digital Life and (separately!) next-gen sequence analysis, but the class has been somewhat random in its topics and train of thought.

Anyway, for the final class I decided I'd go slide by slide through a number of principles that they should apply if and when they find themselves doing computational science. In each case I can point to class exercises and homeworks that illustrate the points, which I think means I haven't totally failed... ;)

Anyway, here's what I have so far:

13 Principles of Computational Science:

1) Computational science is just like any other science: don't trust it if you don't understand it.

Seriously. Computers aren't magic, and computational jargon isn't any more meaningful than any other jargon.
  1. The entire chain of evidence matters.

Keep close track of the raw data; the analysis source code; and the parameters used at each stage of data generation, processing and summarization.

Corollary: Make your raw data available. To do otherwise is just silly.

  1. If it's not automated, it's crrrrrap
As soon as there's some manual step in your pipeline, you've lost track of what you're doing. You may do it differently, or not at all, or incorrectly. And you'll never know. You'll just get different results. Sometimes.
  1. Use version control.
If it's neither raw data (backed up!) nor generated data, put it in version control.
  1. Using other people's software to do science is hard.

They probably had some other use in mind that doesn't fit your needs, but you're going to try to adapt it anyway, aren't you? Good luck with that.

Corollary: using your own software to do science, 2 years after you wrote it, is hard -- because you're not you any more. (Remember, you can never step in the same stream twice.)

  1. No software is trustworthy.
Until you understand your software stack intuitively, have obsessed over parameter choices, and have locked down your software behavior with automated tests, don't trust it. After that, you can grudgingly extend some minimal trust to it, at least until the next version is released.
  1. Computation is not science.
Science is science. Computation may be one of the ways in which you do science.
  1. Hypotheses are good.

It's virtually impossible to analyze data without some kind of hypothesis in mind.

Corollary: Each hypothesis is only a starting point. It's probably wrong, so don't get too attached to it.

  1. More data is not necessarily less confusing.

The more data you have, the harder it can be to get a clean signal. Statistics help here, unless of course you have an unknown systematic bias in your data.

Corollary: You have an unknown systematic bias in your data.

  1. Interdisciplinary research is hard.

You need to be an expert in multiple fields, each with its own special techniques, lingo, and "commonly understood" shibboleths. Proper hypothesis testing involves mastering the first two; publication may depend on avoiding the latter.

Corollary: computational science is implicitly interdisciplinary, hence hard. (If it were easy, we wouldn't need smart people like you to do it, right?)

  1. A lot of computing is just details.
There's very little magical about computing. An awful lot of it is just more details to remember. Running software, gathering the results, processing them, plotting them, tweaking parameters, etc.
  1. Look at your data.
Look at your data, and your results, in as many ways as possible. You'll often be surprised by what's actually in there.
  1. Above all, tell a story.
Nobody is interested in just graphs. If you don't have an interesting story, dig deeper.

I know, somewhat scattered. Any more thoughts, or pointers to similar lists?



p.s. I plan to finish up with my (IMO very underappreciated) principles of How to be a Successful Computational Scientist, summarized here:

  1. Never show them your data.
  2. Do not, under any circumstances, communicate clearly.
  3. Never release your source code, either.
  4. Judge computational science by results, not quality.
  5. Use as much data as possible.

Then they get to fill out evaluations. Whee!

Legacy Comments

Posted by Michael R. Bernstein on 2010-12-10 at 11:50.

Consider moving #3 to after #9, and adding a corollary: "Even if you,
magically, always do things the same way, you should probably consider
your involvement an unknown systematic bias".    Further, there is
probably something missing about making the entire software stack
reproducible if at all possible. It could be considered a corollary
of #1-6 inclusive (except #5, it's actually a corollary to the
corollary). Perhaps make a point about using virtual machines and
backing up their images.

Posted by Noah Spies on 2010-12-20 at 11:10.

"Look at your data.  Look at your data, and your results, in as many
ways as possible. You'll often be surprised by what's actually in
there."    I find people tend not to fully understand this--looking at
data in different ways to them means testing as many hypotheses as
possible by calculating lots of p-values. Before you get down to that
level, it's always helpful to get a feel for the raw data. A human eye
can spot patterns incredibly quickly, and, for example, a little time
spent browsing next-gen sequencing results in the ucsc genome browser
can guide you to ask the right questions.

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