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.
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Notes
REST: Representational State Transfer
HDF5: Hierarchical Data Format Version 5; NWB: Neurodata Without Borders; XML: Extended Meta Language; JSON: Javascript Object Notation
A SimSet is a set of input parameter vectors, each of which is associated with a single simulation. A SimSet may represent many simulations, which will be scheduled to run in parallel on the Simulators in the Simulator Pool. Please see the NeuroManager documents for more details.
Each row in a table has a unique key; a foreign key in a row associates that row with a row in another table. In this way tables support the various characteristics of a thing in a database.
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Acknowledgements
National Science Foundation (NSF-DBI1451032), National Institutes of Health (NIH-G12MD007591) (for use of computational facilities at UTSA).
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Stockton, D., Santamaria, F. Integrating the Allen Brain Institute Cell Types Database into Automated Neuroscience Workflow. Neuroinform 15, 333–342 (2017). https://doi.org/10.1007/s12021-017-9337-x
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DOI: https://doi.org/10.1007/s12021-017-9337-x