Introduction¶

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

Installing SciUnit and NeuroUnit¶

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¶

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):¶

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