The Virtual Brain

"The Virtual Brain" Project (TVB Project) has the purpose of offering modern tools to the Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains, brains modeled at the level of population of neurons.

1. To install TVB code on your machine, we recommend you to first create a dedicated Python env, and afterwards to take our Pypi released packages:

    pip install tvb-library
    pip install tvb-framework
   

2. Alternatively and easier, you could simply download TVB_Distribution from: https://www.thevirtualbrain.org/tvb/zwei/brainsimulator-software. In this variant, you will have Python, TVB and all our 3rd party dependencies downloaded together, you do not need to do anything else other than unzip and double click on tvb_start command.

3. This repository holds the python sources for TVB main codebase. If you clone this repository for extending its functionality, first create a dedicated Python env, select it and then run inside tvb_build folder the following command to link tvb-sources as libraries:

    sh install_full_tvb.sh
   

NOTE:

To contribute to this repo, you are advised to first fork it under GitHub (through the web ui), and next clone that fork on your machine, and use it as you use any other git repository.

More details on our documentation site: http://docs.thevirtualbrain.org.

TVB Scientific library (tvb-library)

"TVB Scientific Library" is the most important scientific contribution of TVB Project, but only a part of our code.

"TVB Scientific Library" is a light-weight, stand-alone Python library that contains all the needed packages in order to run simulations and analysis on data without the need for the entire TVB Framework. This implies that no storage will be provided so data from each session will be lost on close. You need to either persist it yourself in some manner or use the full TVBFramework where HDF5 / database storage is provided as default.

TVB Framework (tvb-framework)

The Virtual Brain framework is a complete framework, wrapped over tvb-library, and offering extra features:

• a plug-able workflow and operations manager;
• a data persistence layer (with a relational DB and H5 File Storage);
• an HTML5 based user interface over CherryPy server;
• visualizers for neuro-science related entities.

You can launch the web interface of TVB with the following command:

python -m tvb.interfaces.web.run WEB_PROFILE

Your port 8080 should be free, as a CherryPy service will try to run there. Your default browser should automatically open http://localhost:8080/ which is the way to interact with TVB Web Graphical Interface.

Testing

For testing our packages, PyTest framework can be used. We also need a few more dependencies for tests specific, which are listed in setup.py files.

Pytest will run all files in the current directory and its subdirectories of the form test_*.py or *_test.py.

The command for running our tests has two forms:

1. Recommendation when working with a git clone of this TVB Github repo:

      cd [folder_where_tvb_framework_is]
      python -m pytest tvb/tests/framework [--profile=TEST_POSTGRES_PROFILE] [--junitxml=path]
      # default profile value is TEST_SQLITE_PROFILE
   
      cd [folder_where_tvb_library_is]
      python -m pytest tvb/tests/library [--junitxml=path]
   

2. The second alternative form of running TVB tests, when installing TVB from Pypi, is:

      pip install -U tvb-framework
      # install optional dependencies needed just for tests (search "extras_require" in tvb_framework/setup.py)
      pip install pytest pytest-benchmark pytest-mock BeautifulSoup4
      pytest --pyargs tvb.tests.framework
   
      pip install -U tvb-library
      # install optional dependencies (from variable LIBRARY_REQUIRED_EXTRA in tvb_library/setup.py)
      pip install h5py pytest pytest-benchmark pytest-xdist tvb-gdist tvb-data
      pytest --pyargs tvb.tests.library
   

• For all the tests to run correctly, the dependencies specified as LIBRARY_REQUIRED_EXTRA in setup.py should be installed
• Make sure that tvb-data package is installed from Zenodo

Coverage

A coverage report can be generated with:

pip install pytest-cov
cd [folder_where_tvb_framework_is]
py.test --cov=tvb tvb/tests/ --cov-branch --cov-report xml:[file_where_xml_will_be_generated]

cd [folder_where_tvb_library_is]
py.test --cov-config .coveragerc --cov=tvb tvb/tests/ --cov-branch --cov-report xml:[file_where_xml_will_be_generated]

Relevant TVB Resources

• For issue tracking we are using Jira: http://req.thevirtualbrain.org
• For API documentation and live demos, have a look here: http://docs.thevirtualbrain.org
• A public mailing list for users of The Virtual Brain can be joined and followed using: [email protected]
• Raw demo IPython Notebooks can be found under: https://github.com/the-virtual-brain/tvb-root/tree/master/tvb_documentation/demos

Acknowledgments

This project has received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement Nos. 785907 (Human Brain Project SGA2), 945539 (Human Brain Project SGA3) and VirtualBrainCloud 826421.