We regularly use a number of analytic tools for computational neurosciences in our research, including brain network analysis and neural simulations. These codes are open source software tools in Python and can be found on the lab's GitHub account.  All routines require NumPy, SciPy and Matplotlib to be installed; some functions optionally use Weave for embedded C++ code.

The implemented routines provide functionality to

  • construct functional networks using different statistical dependence measures
  • calculate graph metrics
  • perform various forms of absolute and relative network thresholding
  • construct random graphs
  • visualize networks in 2D or 3D
  • render the spatial embedding of networks in three-dimensional brain surfaces
  • simulate brain activity using a biological neural population model

The codes for these analytic tools were developed and written by Stefan Fuertinger, PhD, and Joel Zinn, BA. We are offering these codes as a free resource to the neuroscience community. You may redistribute and/or modify them under the terms of the GNU General Public License as published by the Free Software Foundation, version 3 and higher. The codes are distributed without any warranty, including no warranty for merchantability or fitness for a particular purpose (see the GNU General Public License for more details, a copy of which you receive along with each module). Alternatively, you may write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA, or visit their website

If you have questions or comments, please get in touch with us via email or phone at (617) 573-6016.