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YouTube for test tubes

November 23, 2006 By Heidi Ledford This article courtesy of Nature News.

Lights, camera, pipette... online journal aims to put science in pictures.

Cemile Guldal pays attention to details. Her tattoo of a DNA double-helix, for example, doesn't wrap quite all the way around her right arm because doing so would have distorted the major and minor grooves of the helix. And that simply wouldn't do.

So when Guldal, a graduate student at Princeton University in New Jersey, began studying how well different yeast strains invade the medium on which they are growing, she followed the protocols to the letter. But no matter how many times she repeated the experiment, she couldn't produce the results that she saw in published papers.

"For about a year, my boss thought I was completely incompetent because I couldn't replicate those beautiful published pictures," says Guldal. Later, she realized that her troubles stemmed from a basic misunderstanding about how the experiment was performed she had been scrubbing the surface yeast cells from her medium, instead of simply washing it under running water.

Guldal's struggles are precisely what the newly launched Journal of Visualized Experiments (JoVE) strives to stamp out. The fledgling online journal, which started up this month, consists entirely of videos of scientists performing basic molecular-biology protocols.

The journal is the pet project of Moshe Pritsker, a postdoctoral researcher at Massachusetts General Hospital in Boston. Pritsker hopes that JoVE will help scientists to improve the reproducibility of their work, while also providing a window for the public to view what goes on in the lab.

Make or break

Molecular biology is riddled with intricate protocols, and fine details can make or break an experiment. Shake a test tube too vigorously or mishandle a culture and the whole procedure could be ruined. Written protocols often don't spell out critical assumptions. "When a protocol doesn't work, the reason is probably because you're missing some detail," says Guldal. "Nobody really thinks to explain it to you because it seems so trivial. It's routine for them."

Pritsker is not the first to recognize the need for cinematic assistance. Some journals already allow scientists to submit videos to supplement the materials and methods section of their papers. OpenWetWare a biology website that allows participants to add and edit content has a section devoted to protocols and encourages the submission of videos, but has only received five video protocols since the site was founded in 2005.

Nature Protocols also publishes movies as supplementary information to some of its online papers: of about 500 submissions to the journal since its launch in June, more than 20 have included movies. "We've found that, without prompting, when authors sit down to write an exact protocol describing every step they take in a method, they often think of including a movie," says editor Katharine Barnes.

Pritsker wants to encourage that urge by providing a direct incentive for creating videos. Publishing in JoVE gives submitters something that they can specifically list on their résumé. Pritsker hopes to eventually get JoVE articles listed in scientific databases such as PubMed.

"It's a great way to hack into the existing system of publishing," says Sriram Kosuri, a graduate student at the Massachusetts Institute of Technology in Boston and a cofounder of OpenWetWare. "I can easily imagine referencing one of these protocols if I were to write a paper."

Between friends

Publication in JoVE is free. So is watching the videos. The journal currently has no outside funding, but Pritsker hopes to eventually sell advertisements. For now, JoVE runs on a volunteer staff of two Pritsker and his friend, Nikita Bernstein, who provides technical support and a scientific board populated by faculty that Pritsker came to know during his graduate school days at Princeton and his time as a postdoc. The submissions (nine so far) come from his friends and acquaintances. Guldal, for example, was Pritsker's classmate at Princeton.

Pritsker is counting on word-of-mouth to send more submissions his way. His hopes may be grounded in precedence. OpenWetWare, which began as an individual lab website, has grown rapidly over the past year (see ' Online methods share insider tricks').

Guldal has already submitted a video to JoVE illustrating her assays for yeast invasiveness. "I thought this was a good opportunity to set the record straight for these poor graduate students who come along later," she says.

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