Octave: an Open Source Alternative to Matlab Revisited

Neuron to neuron connectivity matrix for the whisker (vibrissae) related somatosensory cortex.
Figure 1. Octave 3.8 graphical interface version displaying neuron to neuron connectivity matrices for whisker related somatosensory cortex (for more about these data see my July 9, 2011 post or the paper “Laminar Analysis of Excitatory Local Circuits in Vibrissal Motor and Sensory Cortical Areas” published January 4, 2011 in PLoS Biology).

More than three years ago on this blog I introduced Octave while writing about brain circuitry data. Octave has come a long way since then. After downloading and a simple setup on your computer you’ll notice two Octave applications. One is the traditional client and the other is the new graphical user interface version, which is slated to be the standard in version 4.

If you’d like to try running the code that displays brain circuitry data like in Figure 1 above, go to the “Laminar analysis of excitatory circuits in vibrissal motor and sensory cortex (Hooks et al. 2011)” record in the SenseLab ModelDB repository and download mhconmatvalues20100928_octave.m from the model files. Place this file in a location you’ll remember.

After starting up Octave-gui you will see a File Browser area in a left area of the application’s window. Navigate to your copy of mhconmatvalues20100928_octave.m and double click on it so that it loads into the editor (in the area to the right). The result should look similar to Figure 1 above without the six graphic display windows. Find the arrowhead (or right-pointing blue triangle) in the editor’s toolbar and click on it. This runs the file displayed in the editor. The six figures defined in the file should display.

Octave is maturing into a very attractive freely available and open source alternative to Matlab. Soon on this blog we’ll look at how easy or difficult it may be to run code written for Matlab in Octave.