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G-Node MATLAB Toolbox

The global scale of neuroinformatics offers unprecedented opportunities for scientific collaborations between and among experimental and theoretical neuroscientists. To fully harvest these possibilities, a set of coordinated activities is required that will improve three key ingredients of neuroscientific research: data access, data storage, and data analysis (...) (Herz et al., 2008)

The G-Node MATLAB Toolbox (GMT) allows convenient access to electro-physiological recordings stored in the G-Node Data Store (Beta) through the MATLAB command line. Requirements are

  • MATLAB R2008b or higher on any platform supporting Java (Linux, Mac, Windows), as well as a

  • G-Node account (user "demo" with password "demo" or a new one available here).

In addition, a backend for persistent and lab-wide caching is recommended but not necessary (e.g., MongoDB).

Installation

Installation of the G-Node Toolbox is similar to that of most MATLAB toolboxes. Follow these steps:

  1. Download and unzip the toolbox or clone it from GitHub via git clone https://github.com/g-node/gnode-client-matlab.git to your local Matlab toolbox directory (for example, $MATLAB_HOME/toolbox)
  2. Adjust the default settings in the default configuration file ($MATLAB_HOME/toolbox/gnode-client-matlab-master/default.json):
    • Set apiDefinition as a path to the supplied requirements.json file. On Linux, for instance, assuming your $MATLAB_HOME corresponds to /home/john/matlab/, you should put /home/john/matlab/toolbox/gnode-client-matlab/requirements.json. On Windows, this should be like C:\\matlab\\toolbox\\gnode-client-matlab\\requirements.json depending on your configuration (Note the double slashes in the path).
  3. Add the Java library to the path by either
    • adding a path to the .jar file ($MATLAB_HOME/toolbox/gnode-client-matlab/lib/client.jar) as the top line in the default Matlab classpath file located usually at $MATLAB_HOME/toolbox/local/classpath.txt (permanently, recommended)
    • or using the javaaddpath function >> javaaddpath('$MATLAB_HOME/toolbox/gnode-client-matlab/lib/client.jar') (valid for only one Matlab session)
  4. Open MATLAB.
  5. Add the toolbox folder to the path either
    • via menu (permanently, recommended) File -> Set Path -> Add Folder.. select $MATLAB_HOME/toolbox/gnode-client-matlab/
    • or using the addpath function: >> addpath('$MATLAB_HOME/toolbox/gnode-client-matlab') (valid for only one Matlab session)
  6. Check that your installation was successful by typing import gnode.*; at the MATLAB prompt. If there are no errors, you can start using the toolbox.
  7. Read the documentation.

Getting started

Before using the toolbox, you should set up your MATLAB environment and initialize a session.

% Move all toolbox functions into scope
import gnode.*;

% Initialize session. 'default' will use the account settings specified
% during installation.
session = init('default');

Now the toolbox is ready for use. It requires a network connection for all operations involving download or upload. The G-Node data store uses a simple object model similar to NEO. All your data is stored in a set of object types tailored to electrophysiology, such as blocks, segments, recording channels, signals et cetera.

In the MATLAB environment, we represent these objects as structures. Here is a basic example for creating and uploading such an object.

% Create a structure containing signal data

signal = make_dummy(session, 'analogsignal');

signal.name = 'My brand new signal';
signal.sampling_rate = struct('units', 'Hz', 'data', 12000);
signal.t_start = struct('units', 'ms', 'data', 0);
signal.signal = struct('units', 'mV', 'data', my_data);

% This returns the ID of the newly created object in
% the G-Node data store

new_object = create(session, signal);

Subsequent object retrieval is equally straightforward and supports various access methods (e.g., single ID, array of IDs, numeric range). Here are a few examples to get you going:

% Lists of objects
my_list = get_list(g, 'analogsignal');

% Single objects
my_recording = get(session, 'analogsignal_947');

% Multiple objects
all = { 'analogsignal_948', 'segment_43', 'unit_8' };
my_recordings = get(session, all);

% Ranges
more_recordings = get_range(session, 'analogsignal', 947, 1002);

More advanced operations (e.g., updates, download queues, batch object creation and upload, and so on) are described in the GMT wiki.

FAQ

Q: Is the G-Node toolbox compatible with older versions of MATLAB (i.e., before R2008b)?
A: Unfortunately not. GMT makes heavy use of the JVM bridge provided by Mathworks. This bridge is under constant development. Various incompatibilities and lack of features make it unfeasible to support MATLAB versions before R2008b.

Q: Is there any versioning support for my data (e.g., revert after destructive edit)?
A: Not yet.

Q: Can I contribute?
A: GMT is open-source; pull requests are always welcome. As a user, please report any bugs or missing features on the Issue Tracker.

License

GMT is distributed under the MIT license (see LICENSE).