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Richard Gerkin, 30 Apr 2014 14:57

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Introduction
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A project highlighting some of the possible interactions between OSB and NeuroElectro/SciUnit
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Installing SciUnit and NeuroUnit
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SciUnit is a pythonic framework for testing scientific models: https://github.com/rgerkin/sciunit.
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NeuroUnit is a library of SciUnit tests and capabilities for neuroscience. https://github.com/rgerkin/neurounit.
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The Neuroelectro API
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Data used for testing models with SciUnit can be obtained in a variety of places. Here we focus on automated testing by pulling electrophysiologal properties of neurons from the literature using NeuroElectro (http://www.neuroelectro.org). The API for grabbing data from NeuroElectro is documented here: http://goo.gl/fuPSu.
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Testing neuroConstruct models with neurounit (sciunit):
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In jython:
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\$ cd \~/neuroConstruct \# Or wherever it is.
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\$ ./nCjython \# Assumes there is a “jython” somewhere in your system path.
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>>> import neurounit.jutils as j
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>>> print j.get\_volts()
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In python:
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\$ cd \~/neuroConstruct \# Or wherever it is.
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\$ python
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>>> import neurounit.putils as p
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>>> data = p.run() \# Opens the bridge to jython.
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>>> volts = data.receive() \# Runs the simulations and receives the data (hangs).
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>>> print volts