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Scientists Continue to Use Outdated Methods

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https://www.the-scientist.com/?articles....d-Methods/

EXCERPT: . . . And TopHat is just one of many out-of-date computational tools to have become embedded as bad scientific habits. Indeed, anecdotal evidence, as well as recent research into the issue, suggest that the use of obsolete software is widespread in the biological sciences community, and rarely even recognized as a problem.

[...] There’s now growing momentum to counter this attitude, as it becomes increasingly obvious that the choice of computational software can have a substantial influence on the progress of science. Not only do users of older methods fail to take advantage of faster and more-accurate algorithms, improved data sets, and tweaks and fixes that avoid bugs in earlier versions, they also contribute to a reproducibility crisis due to differences in the results new and old methods produce.

[...] Studies such as Greene’s and Reimand’s are a reminder that “there’s a difference between software and experimental protocol,” Pachter says. “Changes in computer science are very rapid—the pace of change and nature of change is just very different than it is for experimental protocol.”

But getting that message to researchers is not so simple, he adds. While some responders to Pachter’s December tweet suggested simply removing old tools or old versions of a software online—in order to, at the very least, prevent new downloads of obsolete tools—there are good reasons to retain a record of the computational dinosaurs online. “There is an argument—and it’s an important one—that people may want to reproduce old results or have the ability to run the software as it was at the time,” Pachter says.

Reimand agrees that reproducibility is a key reason to keep good records of older tools....

MORE: https://www.the-scientist.com/?articles....d-Methods/
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