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Journal: Neuroinformatics

Article Title: Integrating the Allen Brain Institute Cell Types Database into automated neuroscience workflow

doi: 10.1007/s12021-017-9337-x

Figure Lengend Snippet: The user can use Python or MATLAB code to access and download the ABI–CTdb’s electrophysiological data and run ABI’s Python SDK routines to extract features from the electrophysiological data. The user can also store them in a local MySQL database that we call “CellSurvey”, use a new extension of our NeuroManager software to run simulations and extract features from them, then compare the simulated and experimental data. The results of these interactions are stored in a second investigation database called “NM–INVdb”. For more details please see the User Guide

Article Snippet: 2 2.3 Extending NeuroManager towards integrated simulation—analysis management Our group has developed an object–oriented MATLAB program called NeuroManager which automates the workflow of simulation job submissions when using multiple heterogeneous computational resources ( Stockton and Santamaria, 2017 , 2016 , 2015 ).

Techniques: Software

Journal: Neuroinformatics

Article Title: Integrating the Allen Brain Institute Cell Types Database into automated neuroscience workflow

doi: 10.1007/s12021-017-9337-x

Figure Lengend Snippet: The ABIApiML classes give access to the ABI Cell Types electrophysiological data from within MATLAB

Article Snippet: 2 2.3 Extending NeuroManager towards integrated simulation—analysis management Our group has developed an object–oriented MATLAB program called NeuroManager which automates the workflow of simulation job submissions when using multiple heterogeneous computational resources ( Stockton and Santamaria, 2017 , 2016 , 2015 ).

Techniques:

Journal: Neuroinformatics

Article Title: Integrating the Allen Brain Institute Cell Types Database into automated neuroscience workflow

doi: 10.1007/s12021-017-9337-x

Figure Lengend Snippet: The local MySQL CellSurvey Database holds features extracted from NWB files downloaded from the Allen Brain Institute Database website. We can use standard SQL queries like these to access the database. The INNER JOINs connect tables in the database, allowing disparate parts of the stored data to be accessed in a single query. The table design is straightforward and is easily seen in the code or by browsing the database with MySQL Workbench. Automating the SQL query employment using custom Python or MATLAB functions is straightforward and easily extended; we have provided a MATLAB wrapper class which is described in Section 3.3

Article Snippet: 2 2.3 Extending NeuroManager towards integrated simulation—analysis management Our group has developed an object–oriented MATLAB program called NeuroManager which automates the workflow of simulation job submissions when using multiple heterogeneous computational resources ( Stockton and Santamaria, 2017 , 2016 , 2015 ).

Techniques:

Journal: Neuroinformatics

Article Title: Integrating the Allen Brain Institute Cell Types Database into automated neuroscience workflow

doi: 10.1007/s12021-017-9337-x

Figure Lengend Snippet: MATLAB access of CellSurvey database. The MATLAB class ABIFeatExtrData provides access to the local CellSurvey database of features extracted from the public online ABI Cell Types database

Article Snippet: 2 2.3 Extending NeuroManager towards integrated simulation—analysis management Our group has developed an object–oriented MATLAB program called NeuroManager which automates the workflow of simulation job submissions when using multiple heterogeneous computational resources ( Stockton and Santamaria, 2017 , 2016 , 2015 ).

Techniques: