Tuesday, April 15, 2008

Data and the Open Source Paleontologist - Teaser

First, an assignment for all readers: Fill out a survey sponsored by NESCent (National Evolutionary Synthesis Center and the UNC Chapel Hill Metadata Research Center, who are aiming to establish a data repository for data underlying published work in evolutionary biology and related fields. The deadline is April 16, so act fast!

This is your chance to offer input on how you use and distribute original research data. Every researcher should have a stake in this. The survey took me about 10 minutes to fill out, and the questions were pretty basic (how often do you get requests to share data? What format are your original data in? What happens to your data after you publish?).

Why is this important? I'm going to cover this in more detail in a future post (hopefully in the next day or two). In brief, transparency is at the heart of reproducibility and testability, which are the basis of science. With more journals pushing research data to "supplementary information," and more scientists working in the digital realm, we have opportunities and problems to confront.

More to come. . .


Mike Taylor said...

Hey, Andy. I need to edit a Nexus data file. In the past, I've used NDE (the Nexus Data Editor) on Windows, but now that I'm no longer running VMWare, I don't really have that option. What would you recommend for Unix/Linux?

Andy said...

My Nexus data editor of choice is Mesquite. Quite a few more features than NDE, so a little slower to run sometimes, but overall worth the switch. Plus, it has all sorts of other nifty tools.

Mike Taylor said...

Hmm. I've used Mesquite a few times, and found it appallingly slow and clumsy, with its constant bloom on new windows showering the screen, and its inexplicable random pauses. Not a fan :-)

But I had a very happy surprise when I tried installing and running NDE under WINE, and found that it Just Worked first time. In my so-far limited experience of WINE, it's a winner: maybe you'll do an article on it some time?

Andy said...

The latest version of Mesquite has solved the windows-run-amok problem, putting a lot of the clutter into tabs. Its speed is still relatively slow on some areas, but I still really love a lot of the character analysis options (particularly the ability to calculate phylogenetically independent contrasts).

Sure, a post on Wine should be forthcoming at some point (although it's a little further down the list, after open sourcing research data and the long-promised post on Slicer).