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Hackathon Launches API for Public Neuroscience Dataset

June 26th, 2012 Gavin Corley Genetics, Net News, Neurology, News

The Allen Institute for Brain Science, a nonprofit medical research organization in Seattle, Washington, has released an application programming interface (API) to allow scientists and programmers to create new software to traverse their growing database of neuroscience data.

The Allen Institute is developing a growing database of gene expression and neuro-anatomical data with a size currently in the order of petabytes (millions of gigabytes). All of the data is publicly available through the Allen Brain Atlas Resources website.

The API is essentially a set of development tools which enable easier access and sharing of the public database. It provides a powerful way to access data across species, ages, disease and control states, allowing for data analysis across data types and samples. According to the website, the API includes access to the following datasets:

  • High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images
  • 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain
  • Primary microarray results for the Human Brain and Non-Human Primate
  • RNA sequencing results for the Developing Human Brain
  • MRI and DTI files for Human Brain

The API contains the following resources:

  • RESTful model access
  • Image download service
  • 3-D expression summary download service
  • Differential expression search services
  • NeuroBlast correlative searches
  • Image-to-image synchronization service
  • Structure graph download service

The API was launched last week at a hackathon hosted by the the Allen Institute for Brain Science. The event was attended by scientists and programmers from industry and academia. Source code from the event will be released through the Allen Brain Atlas data portal during their next public data release next October and through the  International Neuroinformatics Coordinating Facility website.

Press release: First Ever Allen Brain Atlas Hackathon Unleashes Big Data API to Push Neuroscience Forward…

Flashbacks: Allen Brain Atlas Completed; Mouse Spinal Cord Gene Map Goes Online; BrainNavigator, An Online Atlas to Browse Brain Structures

Gavin Corley

Gavin holds a first-class Bachelor’s degree in Electronic Engineering degree from the University of Limerick and a Ph.D. in Biomedical Engineering from the National University of Ireland, Galway. He is currently a post-doctoral research and project leader at the NUI Galway where he has spent the last 2 years leading the product development and commercialization of two novel technologies for the management of varicose veins and chronic venous leg ulcers. He has published several research papers in the fields of anatomy, physiology and medical physics and is the lead author of one patent application to date. In his free time Gavin has been known to swim, cycle and hum a tune or two.

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