Neuroscientists don't talk to each other enough, say the creators of the Whole Brain Catalog.
That may seem like an odd sentiment here at the annual Society for Neuroscience meeting, where more than 32,000 neuroscientists and their colleagues have converged in Chicago to update each other on recent findings and spark new ideas. But researchers at the University of California, San Diego, aren't concerned about the kinds of information that can be easily pasted into a PowerPoint presentation or a poster--they worry about massive sets of useful data languishing away in laboratory backrooms because brain scientists don't have good ways to deal with them.
"There's a lot of data out there that just sits on people's hard drives, because we don't have a place where people can really get to it right away," says Stephen Larson, who helped create the software tool as part of his Ph.D. thesis work. "The open-source neuroscience community has not been as strong as it could be. We wanted to energize that community."
Larson and his colleagues’ solution took root from an unlikely source: video games. Aiming to create an appealing graphical interface for their program, the team turned to Java Monkey Engine, a 3-D gaming engine. The result is a free, open-source brain visualization program that allows scientists to upload, share and comment on all manners of brain data. "[JME] been used for entertainment up until now," Larson says. "But we thought it could be very useful for science visualization."
UCSD's robust information infrastructure provided another key component to getting the program off the ground. To use the Whole Brain Catalog, scientists upload their data--which can easily exceed tens of gigabtyes--onto a dedicated server set up by the catalog team using seed money from the Wiatt Family Foundation. The visualization software then remaps the data against standard models of the brain and serves it up from UCSD computers in a manner similar to Google Maps.
The application's scope is anything but modest. It is designed to work at all levels, incorporating 2-D photos of large brain slices as easily as it can add individual molecules imaged in three dimensions using electron microscopy. And it's not just static data--it can use sequences of images to render detailed simulations of brain activity. One popular demonstration at the catalog's booth is an animation of new neuron growth in the dentate gyrus, based on data from a recent Neuron paper.
Researchers also have plenty of options for data already in the system. Uploaders can decide whether they want to keep the data private for the time being or make it open for everyone to see. A robust annotation program allows anyone to make comments on noteworthy items and ensures that the data is always tagged with the name of the person who uploaded the data. The database is searchable by keyword, and allows researchers directly overlay other people's data onto their own. Easy ways to pull up gene expression data from the Allen Brain Atlas and direct links to Neurolex, a Wikipedia-like database of brain science terms relevant to researchers, are included.
The developers seem to be on target. Interest in the Whole Brain Catalog, which debuted in a beta form here at the conference, has been pretty high. Despite the hubbub of the meeting, several scientists have been so impressed that they have already taken time out of their schedules to upload their data, Larson says.
"This is not going to be the solution to all our issues with data," he adds. "But making it very graphical, very visual, is going to open up and help us solve many problems in neuroscience."
--Aalok Mehta
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