Archive for September, 2013

Hiring computational biologists

25 Sep 2013

The Morgridge Institute for Research (MIR), a private research institute associated with UW-Madison, is looking to hire some computational folks working in biology. One position is joint with my department, Biostatistics & Medical Informatics.

Yet another symposium

Yesterday afternoon, they held a symposium on “Computation in Biology” (Here’s the agenda.) Great speakers: Marc Suchard, Brian Shoichet, David Page, and Winston Hide. They were asked to speak broadly about computation in biology and on the key issues for the future, and there was plenty of time for discussion.

I’m not sure what MIR was hoping to get out of the symposium, but if they were looking for guidance regarding their hiring efforts, it wasn’t effective. At the beginning, the discussion was quite heated but not terribly constructive. In the middle, it became more like the usual sort of question/answer after a seminar. I must admit I didn’t stay to the end. Perhaps some important insights were gained after I left. But it seems unlikely that the symposium provided much guidance about hiring in computational biology.

The key issues

Here are what I think the key issues are, when a scientific organization is looking to hire some computational folks.

  • Do you want a targeted search (for particular kinds of applications or approaches), or do you want to leave it general and just pick the best folks who apply?. (In my experience, targeted searches don’t work as well; you miss out on some great people.)
  • What service role is expected of the person? Do you want them to meet some particular scientists’ needs, or are you going to let them do whatever they want, with the hope that they form useful (to the organization) collaborations? (The expectations should be made explicit.)
  • At promotion time, who is going to evaluate the person? If it’s a separate academic department (say, Statistics, or maybe Biochemistry), do they share your organization’s values? (Some of the best applied computational scientists may not be generating the NIH grants that a traditional biological sciences department might expect, nor the JASA or Biometrics papers that a Statistics department might expect.)
  • Will the person have appropriate mentors? Is there anyone at the institution who really understands the nature of their position and what they need to do to succeed? (I worry particularly about computational scientists who are isolated from their computational peers.)

I don’t have any great answers, but those are the issues that I’m concerned about.

Update: The real point I’m trying to make: academics doesn’t do a good job of rewarding tool building (eg, software tools). It’s often viewed as better to write papers with toy implementations than to make generally useful software. That’s a real problem for computational biology, and for folks seeking to hire truly useful computational biologists.

Code review

25 Sep 2013

There was an interesting news item in Nature on code review. It describes a project by some folks at Mozilla to review the code (well, really just 200-line snippets) from 6 selected papers in computational biology.

There are very brief quotes from Titus Brown and Roger Peng. I expect that the author of the item, Erika Check Hayden, spoke to Titus and Roger at length but could just include short bits from each, and so what they say probably doesn’t fully (or much at all) characterize their view of the issue.

Titus is quoted as follows, in reference to another scientist who retracted five papers due to an error in his code:

“That’s the kind of thing that should freak any scientist out…. We don’t have good processes in place to detect that kind of thing in software.”

Roger is quoted at the end, as follows:

“One worry I have is that, with reviews like this, scientists will be even more discouraged from publishing their code…. We need to get more code out there, not improve how it looks.”

I agree with both of them, but my initial reaction, from the beginning of the piece, was closer to Roger’s: We often have a heck of time getting any code out of people; if we are too hard on people regarding the quality of their code, they might become even less willing to share.

On the one hand, we want people to produce good code:

  • that works
  • that’s readable
  • that’s reusable

And it would be great if, for every bit of code, there was a second programmer who studied it, verified that it was doing the right thing, and offered suggestions for improvement.

But, on the other hand, it seems really unlikely that journals have the resources to do this. And I worry that a study showing that much scientific software is crap will make people even less willing to share.

I would like to see the code associated with scientific articles made readily available, during the review process and beyond. But I don’t think we (as a scientific community) want to enforce rigorous code review prior to publication.

Later, on twitter, Titus took issue with the “not improve how it looks” part of what Roger said:

“.@kwbroman @simplystats @rdpeng Please read you are deeply, significantly, and completely wrong about code review.”

Characterizing code review as strictly cosmetic was an unfortunate, gross simplification. (And how code looks is important.)

I don’t have enough time this morning to really clean up my thoughts on this issue, and I want to get this out and move on to reading that dissertation that I have to get through by tomorrow. So, let me summarize.


We want scientific code to be well written: does what it’s intended to do, readable, reusable.

We want scientific code to be available. (Otherwise we can’t verify that it does what it’s intended to do, or reuse it.)

If we’re too hard on people for writing substandard code, we’ll discourage the availability. It’s an important trade-off.

Department websites

11 Sep 2013

I was thinking about department websites, partly because my own department’s website is terrible, and recently a colleague asked me whether I could suggest some good department sites.

I’ll describe the basic principles for a good department website, and then I’ll comment on a number of examples.

But first: No discussion of academic web pages is complete without referring to the xkcd comic on University websites, so let’s start with that:

xkcd comic: University Websites