Eclipse Install or IntelliJ Install or Gradle Install | How to Contribute | What are all the files here for?

WalnutiQ

"Time is all you have. And you may find one day that you have less than you think."

~ Randy Pausch

Welcome! WalnutiQ is a human brain model simulation in Java. The goal of this repository is to store code that can simulate a full sized human brain in real-time. A real intelligence machine built on biological principles will be able to solve many of the problems which currently plague the world and allow us to unravel the mystery of human conciousness. It will be a long journey but this has the potential to dramatically change the world for the better.

Here you will find code that allows you to build a partial human brain model, train it on input data using theorized learning algorithms, and view its activity as text output. All of the code here supports modeling of the human brain at a high level of abstraction while still allowing user access to individual neuron properties. For more information please watch this video playlist to become familiar with the neuroscience behind this repository.

If you are interested in becoming a researcher/developer, the only requirement is interest in understanding how the brain really works. If you are not interested in programming there are plenty of research tasks we need your help on here. If you are interested in gaining programming experience by building brain models I would be happy to google hangout with you or meet you in person regardless of your programming experience! Feel free to e-mail me at quinnliu@vt.edu to get coffee/lunch/dinner to talk about how you can contribute.

Most importantly, this research is made possible by the neuroscientists and engineers at Numenta. Numenta has designed a exciting new technology that accurately models layers 3 & 4 of the human neocortex. They have generously released the pseudocode for their learning algorithms, and this repository is an extended implementation of their algorithms using object-oriented programming. Make sure to read Numenta's great explanation of their research in this white paper to better understand the theory behind this repository.

Setup in Linux/Mac/Windows with Eclipse

Install Eclipse Standard 4.3.2 or use any other version of Eclipse if you already have it installed.
Go to the top right of this page and hit the Fork button. Then clone your forked WalnutiQ repository locally. Then import it as a Git project into Eclipse. Right-click your package explorer => Import... => Git => Projects from Git => Next > => Existing local repository => Next > => Add... => Browse to the WalnutiQ folder you cloned locally and finish.
IMPORTANT: You will notice that your folders will have red X's everywhere. To fix this right click your src folder then hover over "New", then click "Source Folder". Then give it the "Folder name:" src/main/java. Right click your src folder again and hover over "New", then click "Source Folder". Then give it the "Folder name:" src/test/java Similarily for the folder experiments right click the folder and go to New => Source Folder => Folder name: experiments. Finally for the folder images right click the folder and go to New => Source Folder => Folder name: images.
In Eclipse, add all the libraries (.jar file) in the folder referencedLibraries/ by right-clicking your folder WalnutiQ in the package explorer => Build Path => Add External Archives...
In Eclipse, add JUnit 4 by right-clicking your folder WalnutiQ in the package explorer => Build Path => Add Libraries... => JUnit => Next > => Finish
In Eclipse, also add JRE System Library by right-clicking your folder WalnutiQ in the package explorer => Build Path => Add Libraries... => JRE System Library => Next > => Finish
Right click your folder WalnutiQ => Run As => JUnit Test => ALL TESTS PASS!

Setup in Linux/Mac/Windows with IntelliJ

Install IntelliJ IDEA 13.1 FREE Community Edition or use any other version of IntelliJ if you already have it installed.
Go to the top right of this page and hit the Fork button. Then clone your forked WalnutiQ repository locally.
Open up IntelliJ and click "Import Project" => Select "Gradle" => Next => Select "Use default gradle wrapper (recommended)" => Finish
In IntelliJ right-click the WalnutiQ/ folder and select "Run 'All Tests'". You can also run your tests through the terminal with the command ./gradlew build when inside the WalnutiQ/ folder.

Setup in Linux/Mac/Windows with Gradle

Go to the top right of this page and hit the Fork button. Then clone your forked WalnutiQ repository locally. Navigate into the WalnutiQ/ folder.

To run all of the code in the Linux or Mac terminal type:

prompt> ./gradlew build
:compileJava UP-TO-DATE
# some other stuff...
:build UP-TO-DATE

BUILD SUCCESSFUL

To run all of the code in the Windows terminal type:

prompt> gradlew.bat
# some other stuff...

BUILD SUCCESSFUL

If you see BUILD SUCCESSFUL all of the tests have passed!

How to Contribute

View an example of how some of the code is used in the file NoiseInvarianceExperiment.java. Please do not be afriad to ask a question if you are confused!
View our issue tracker and create a new issue with a question if you are confused. Otherwise, assign a issue to yourself you would like to work on or suggest a new issue if you kinda know what you are doing.
For now we are using the Git workflow model described here to contribute to this repository effectively. Happy coding!

What each file/folder in this repository is for:

experiments
- model
  - MARK_I
    - vision = experiments with partial visual pathway models on a popular handwritten digit data set called MNIST
gradle = the actual Gradle code for building our Java code
images = images used in training & testing the partial brain model
modelInOtherObjectOrientedLanguages = I realize not everyone is the biggest fan of Java so let's rewrite it in as many other object oriented languages as possible!
referencedLibraries = contains .jar files(of other people's code) needed to run WalnutiQ
src
- main
  - java
    - model
      - MARK_II = the core logic for the partial brain model. Includes abstract data types for basic brain structures and learning algorithms that simulate how the brain learns.
        
        connectTypes = allow the different brain structures to connect to each other in a variety of ways
        
        parameters = allows construction of different WalnutiQ models from command line for this repo https://github.com/quinnliu/CallWalnutiQ
        
        SpatialPooler.java = models the sparse & distributed spiking activity of neurons seen in the neocortex and models long term potentiation and depression on synapses of proximal dendrites
        
        TemporalPooler.java = models neocortex's ability to predict future input using long term potentiation and depression on synapses of distal dendrites
      - util = classes that enable the brain model properties to be viewed graphically and efficiently saved and opened
- test = test classes for important classes in the src/main/java/model folder
.gitignore = contains names of files/folders not to add to this repository but keep in your local WalnutiQ folder
.project = when writing your code using Eclipse this file will allow all of your files to be organized in the correct folder
.travis.yml = tells our custom travis testing site what versions of Java to test the files here
BrainTheories.md = list of important brain theories with support and simple explanation
LICENSE.txt = MIT liscense saying you can do whatever you want the code here but it would be very cool of you to do something nice with it.
README.md = the file you are reading right now
build.gradle = compiles all of the code in this repository using Gradle
gradlew = allows you to use Gradle to run all of the code in this repository in Linux & Mac
gradlew.bat = allows you to use Gradle to run all of the code in this repository in Windows
settings.gradle = specify which projects to include in our Gradle build