Introduction

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A project highlighting some of the possible interactions between OSB and NeuroElectro/SciUnit

Installing SciUnit and NeuroUnit

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SciUnit is a pythonic framework for testing scientific models: https://github.com/rgerkin/sciunit.

NeuroUnit is a library of SciUnit tests and capabilities for neuroscience. https://github.com/rgerkin/neurounit.

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.

Testing neuroConstruct models with neurounit (sciunit):

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In jython:

\$ cd \~/neuroConstruct \# Or wherever it is.

\$ ./nCjython \# Assumes there is a “jython” somewhere in your system path.

>>> import neurounit.jutils as j

>>> print j.get\_volts()

In python:

\$ cd \~/neuroConstruct \# Or wherever it is.

\$ python

>>> import neurounit.putils as p

>>> data = p.run() \# Opens the bridge to jython.

>>> volts = data.receive() \# Runs the simulations and receives the data (hangs).

>>> print volts