chuttenhower's blog

All talk and no action

This article is 100% true, yet at least 90% useless - if you look closely, they barely offer any practical solutions to the problem. Scientific software development is little different from experimental protocol development and execution; there's no substitute for expertise, attention to detail, and lots of time and effort.

Computational science: ...Error: why scientific programming does not compute

Quality, quantity, and academic promotion

After my last detail-oriented post, I thought I'd write about something more abstract; on a day like today, something like coincidences or binary arithmetic might be appropriate. But apropos to the topic actually at hand, life goes on pretty much as usual here, both today and tomorrow. Academia is infamous for its Byzantine promotion criteria, and it's striking how many of them boil down to quantity versus quality.

Organizational software and computational tools

There's essentially no topic that I'd like to discuss here that I wouldn't also be happy to discuss multiple times. Like everyone, my approaches to any particular organizational task or scientific problem change over time, and the resources, technologies, and prevailing opinions within the community (particularly the bioinformatics community) are constantly in flux. I've spent part of this weekend reorganizing my personal file space and directory layout, since data and document locations were getting out of hand, but I'd rather not discuss the new system until it's had time to sink in a bit. Besides, Bill Noble's written an excellent piece in PLoS CB that deals more fully with the architecture and philosophy of project organization. Instead, I'll mention some of the software tools I use for organization in general, thus guaranteeing myself not one but two follow-up topics (one on the new filesystem layout, and one when this entry is inevitably outdated).

Responding to reviews

Tuesday Science just doesn't have the same ring to it, does it? I'll have to keep myself honest about this - although if that video repost doesn't buy me an extra few days of leniency, I don't know what does. How often do we run into something that scientifically domain-specific and funny?

For reasons that will hopefully soon cease to be relevant, we've been dealing this week with responding to, rather than writing, reviews. Despite the fact that I really do view reviews as fluid conversations between authors, referees, and editors, I find that the process of responding to reviews involves a substantially different mindset than writing one in the first place. The reasons are probably both obvious and irrelevant. When writing a review, you're squeezing out a bit of time to deal with a situation that's been unwantedly thrust upon you. You're an outside observer, and unless you've already seen the work presented (which, admittedly, is the most commonly targeted review situation), you're likely to start out pretty dubious. You're like a child who wanders into the middle of a movie.

It's funny because it's true

Present collaborators excluded, of course!

Reviews

Another piece of academic logistics that's been of interest in the lab lately has been how to effectively referee a manuscript. On the surface, this is a relatively straightforward process: a journal emails you, you reluctantly hit "Agree", and two weeks plus one day later when you receive an automated email reminding you that you're late, you hastily dash off a few sentences deriding the document as the worst piece of drivel to ever disgrace your inbox. Well, at least that's the way it goes if you happen to be the third reviewer.

Welcome and creating a scientific poster

Welcome to the inaugural installation of Sunday Science! For those who don't already know, my lab here at HSPH has been slowly ramping up since I started last summer. Now that there's a really great group of people helping me out here, I'd like to take the time to work on some fun projects in between grantwriting. That includes posting articles here in an effort to capture in organized form questions, thoughts, or (remarkably) actual science that's come up over the past week. I'll be keeping myself honest by posting each Sunday - hence, Sunday Science. Because we never get a day of rest in academia anyhow, right?

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