Hackathon Launches API for Public Neuroscience Dataset

Hackathon Launches API for Public Neuroscience Dataset

June 25, 2012 — The Allen Institute for Brain Science convened the first ever Allen Brain Atlas Hackathon last week, opening its doors to a diverse group of programmers and informatics experts for a non-stop week of collaboration, learning and coding based on its public online platform of data, tools and source code. The event brought together more than 30 participants from top universities and institutes ranging from the Baylor College of Medicine in Houston to the Nencki Institute of Experimental Biology in Poland, as well as from start-ups and established technology companies, to develop data analysis strategies and tools based on the newly enhanced Allen Brain Atlas application programming interface (API).

“This hackathon stems from our longstanding, open approach to science and our belief that putting our data-rich resources in the hands of the many and varied experts around the globe is the most effective way to drive progress in brain research,” said Chinh Dang, Chief Technology Officer of the Allen Institute for Brain Science. “The hackathon projects delivered innovative ways of handling data, offering direct contributions to the informatics and programming communities as well as to neuroscience. We hope that this event serves as a springboard for others out in the community to use our API, and we look forward to seeing what can be done with it.”

The Allen Institute for Brain Science is one of the biggest data producers in neuroscience, with rapidly growing data stores in the petabyte range that it makes publicly available through its Web-based Allen Brain Atlas resources (www.brain-map.org). These resources include, among others, anatomically and genomically comprehensive maps of genes at work in the mouse and human brains and receive approximately 50,000 visits each month from researchers around the globe.

The public API was created as an additional form of data sharing to spur community technology development and further empower scientists to make groundbreaking discoveries about the brain in health and disease—including insights into learning, cognition, development, Alzheimer’s, obesity, schizophrenia, autism, and more—that will deliver better treatment options sooner. The hackathon coincided with the public release of the full Allen Brain Atlas API earlier this month, and a key goal of the event was to ignite community momentum and interest in using it.

Using the Allen Brain Atlas API, developers can create entirely new software applications, mashups and novel data mining tools for making sense of the large and ever-growing volumes of neuroscience data. The API offers data access across species, ages, disease and control states, providing a powerful means to compare many types of data (e.g., histology images, gene expression, and MRI) among many types of samples (e.g., ages, species or diseases).

“The Allen Institute is a leader in large-scale open science, known for providing high-quality data and online tools that advance brain research,” said Sean Hill, Executive Director of the International Neuroinformatics Coordinating Facility (INCF). “With the Allen Brain Atlas Hackathon and their public API, they are bringing the same collaborative, community-focused approach to technology development and innovation that is at the core of INCF’s mission.”

The hackathon program was designed to provide scientists and programmers a solid foundation in using the Allen Brain Atlas API for data mining, data analysis and tools development. The event featured a handful of speakers from the Allen Institute, as well as external experts who had leveraged earlier versions of the API in their work. As a hands-on workshop, participants spent most of the time working on projects of their choice. The Allen Institute development team actively participated throughout the week to provide specific examples of API usage, as well as to team up with community participants to develop collaborative projects. Participants’ presentations throughout the week showcased their projects and progress, stimulating new ideas and benefiting from the collective feedback and troubleshooting power of the entire group.

Projects ranged from practical applications, such as using a list of glioblastoma-related genes to discover biological patterns that could shed new light on the biology of the disease and developing strategies to use gene expression data with functional brain scanning technologies, to purely creative applications, including translating genomic data into music.

Source code from participants’ projects will be made publicly available on the Allen Brain Atlas data portal (www.brain-map.org) as part of the Allen Institute’s next public data release in October, as well as a through the INCF website (www.incf.org).

The Allen Brain Atlas Hackathon was hosted by the Allen Institute for Brain Science and funded jointly with the International Neuroinformatics Coordinating Facility (INCF).

Web-based brain atlas, a project by the Allen Institute for Brain Science, has been completed. The institute was established and financed by Microsoft co-founder Paul Allen. The atlas, available to anyone for free, is a three-dimensional map of 21,000 genes expressed in the brain of a mouse.

Since humans share more than 90 percent of their genes with mice, the Atlas offers profound opportunity to further understanding of human disorders and diseases such as Alzheimer’s, Parkinson’s, epilepsy, schizophrenia, autism and addiction. About 26 percent of American adults — close to 58 million people — suffer from a diagnosable mental disorder in a given year…

“This project is an unprecedented union of neuroscience and genomics,” said philanthropist and Microsoft co-founder Paul G. Allen, who provided $100 million in seed money to launch the Allen Institute for Brain Science and its first project, the Allen Brain Atlas, in 2003. “The comprehensive information provided by the Atlas will help lead scientists to new insights and propel the field of neuroscience forward dramatically…”

The project has already led to several significant new findings about the brain. It reveals that 80 percent of genes are turned on in the brain, much higher than the 60 to 70 percent scientists previously believed.

It indicates that very few genes are turned on in only one region of the brain — paving the way for additional insight about the benefits and potential side effects of drug treatments. And it shows the location of genes associated with specific functions, providing scientists with valuable information about regional brain activity…

The Atlas gives scientists worldwide the gift of time, providing in one place an enormous database of information that an individual researcher could spend a lifetime trying to gather.

Many of the discrete regions of the brain perform similar functions in all mammals, and greater than 90 percent of all mouse genes have a direct counterpart in humans. By establishing this baseline of the normal mouse brain, the Atlas allows researchers to compare the brain with others altered to mimic neurological and psychiatric diseases found in humans.

Previous atlases have contained anatomic maps showing the location of various regions of the brain, but little or no information about the gene activity within them. Others have contained gene information but none have been nearly as comprehensive as the Atlas, which includes data for every major structure in the brain for nearly all the genes in the genome.

Even before its announced completion, the Atlas was receiving more than 4 million hits monthly and being accessed by approximately 250 scientists on any given work day. Users are not required to provide information about their work, but anecdotal evidence indicates that the Atlas is already assisting research projects.

“I use it around the clock, night and day. My whole lab does,” said Stanford University neurobiology professor Ben A. Barres, who is using the Atlas to confirm his team’s findings about glial cells, a type of non-neuronal cell within the nervous system.

“It’s completely essential. It’s saved us years and years of work, maybe decades. We could never have done all this, either financially or in terms of the amount of labor and time. It was just so incredibly generous of Mr. Allen to do this, and I think it’s hard to even overstate what the payoff is going to be for research.”

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.

Source : http://www.alleninstitute.org/Media/documents/press_releases/2012_0625_PressRelease_Hackathon.html

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