Title |
Integrating the Allen Brain Institute Cell Types Database into Automated Neuroscience Workflow
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Published in |
Neuroinformatics, August 2017
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DOI | 10.1007/s12021-017-9337-x |
Pubmed ID | |
Authors |
David B. Stockton, Fidel Santamaria |
Abstract |
We developed software tools to download, extract features, and organize the Cell Types Database from the Allen Brain Institute (ABI) in order to integrate its whole cell patch clamp characterization data into the automated modeling/data analysis cycle. To expand the potential user base we employed both Python and MATLAB. The basic set of tools downloads selected raw data and extracts cell, sweep, and spike features, using ABI's feature extraction code. To facilitate data manipulation we added a tool to build a local specialized database of raw data plus extracted features. Finally, to maximize automation, we extended our NeuroManager workflow automation suite to include these tools plus a separate investigation database. The extended suite allows the user to integrate ABI experimental and modeling data into an automated workflow deployed on heterogeneous computer infrastructures, from local servers, to high performance computing environments, to the cloud. Since our approach is focused on workflow procedures our tools can be modified to interact with the increasing number of neuroscience databases being developed to cover all scales and properties of the nervous system. |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 23 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 6 | 26% |
Other | 4 | 17% |
Researcher | 4 | 17% |
Professor > Associate Professor | 3 | 13% |
Student > Doctoral Student | 1 | 4% |
Other | 3 | 13% |
Unknown | 2 | 9% |
Readers by discipline | Count | As % |
---|---|---|
Neuroscience | 9 | 39% |
Computer Science | 4 | 17% |
Engineering | 3 | 13% |
Immunology and Microbiology | 1 | 4% |
Biochemistry, Genetics and Molecular Biology | 1 | 4% |
Other | 2 | 9% |
Unknown | 3 | 13% |