Cortex Files

Installation
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Ubuntu, Fedora, Windows XP
	Extract the files to a directory
	Download the Samples and copy them into Cortex/Output/Spiking
	Start Cortex and try...	

Mac OSX
	Extract the Application and copy it to your Applications Directory
	Upon the first start Cortex will copy the Samples and Config files into Library/Application Support/Cortex
	Download Samples (Beta2) and copy them into Library/Application Support/Cortex/Output/Spiking

Usage
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For the beginning it is probably the easiest way to just open a sample simulation file (extension ".cortex").
For this purpose just select the blue "L" on the toolbar or from the menu File->Load.
The yellow toolbar "W" allows you to change Neuroncount, WeightNames, Save and Load other WeightMatrices.
The yellow toolbar "T" allows you to define the basic trial setup: How many stimulus phases, bias, distractor, etc. 
If you configure your own set of trials just enter sample configurations. More samples and shuffling of the trial sequence can be configures later (Yellow S)
The concrete values for Lambdas, Weights and other Parameters are configured via the yellow C.
Further options are available with the yellow S (Simulation Setup) and M (Meanfiled setup).
With the coloured "S" you start a simulation and with the coloured "M" a Meanfield approximation.
Cortex should tell you if something is missing (Of course: Bugs are possible :-)
The toolbar provides various other funtions: Just try.
An important feature is available via the Menu Application->LoadLibrary. Here you will find some exaample libs to load which might extend your calculations on you specific simulations. After loading additional toolbar buttons are available. 
Blue "p" and "C" buttons show the output of the Neuron_Module *only* after a simulation was started not when only loading.
The big advantage of this application might be that you can see the outcome of a parameter change very quick and easy.
The direct spiking output is stored as well (see open issues below) for further graphical usage. (Filename.cortex.spikes)
During the simulation the update of the window is done once per trial phase, hence be patient. (This can of course be optimized as many other things).
MAC and WIN Unfortunately the Sample Simulations might be loadable only after some file name conversion "Lambda" issue - see below. 
If you decide that the program is useful, please download the sources via the SVN repository.
RapidSVN is an application available on many platforms.
Example Workspace files for Codeblocks are provided within the SVN repository as well as some development information.

Open Issues
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There are many...
- be careful  with the selection of response functions; they are very special and require (so far) some coding adaptions
- ideally all functions for the calculation of model responses should be configurable more flexible or even as well dynamic applications
- We should find a better solution for the file names
- Test, Test, Test: There might be some more bugs...
- Hence consider the application as a "Prototype" and see how to make it better.
- On Mac OSX we need  to ensure subdirectiory structure for "SharedSupport"!
- Cortex was developed entirely on notebooks; hence some testing on really big screens would be useful
- so far I did not do any check for memory leaks...
- be aware of possible inconsistencies and sudden crashes!
- The spike output is stored in an additional file with the same name and extention ".spikes". Very long filename and inconsistencies possible!
- On Mac OSX and Windows I really ran into heavy problems with "Lambda" in file names - we should not do this...
- Create further SVN branches for more developers
- Coordinate the programming to comprise a basic line for the main application and a plugin "line" - hence extend the API.
- After all: other software to calculate neuronal dynamics should be easy to integrate and hence respective further options would be possible.
- Further more: Set up the Bug tracker....
- More intensive testing on the "non-primary" platforms might be necessary (primary development with Ubuntu)
After all: If you consider the program useful please download the SVN repository and adapt it to your needs!


For now (Beta): That's it. 
Innsbruck, 29.3.2011
Anja (anja.stemme@gmx.de)