Required Software

Day 1 (Identifying flexible pockets and neural network scoring methods/POVME and NNScore) include hands-on tutorials that require certain free software programs:

• Python 2.X: https://www.python.org/downloads/
• NumPy and SciPy: http://www.scipy.org/scipylib/download.html
• matplotlib: http://matplotlib.org/downloads.html
• VMD: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
• Tutorial scripts and files: https://www.dropbox.com/s/2fzfsw8isqc9q39/Tutorials.zip?dl=0

Installing the Software on Your Laptop

You’re welcome to install each of these software packages individually on your own laptop, but installation can be challenging on some systems. We recommend downloading a prepared VirtualBox image of Ubuntu with everything pre-installed.

1. Download and install the Oracle VirtualBox platform package for your operating system: https://www.virtualbox.org/wiki/Downloads
   • For Windows, detailed instructions can be found here: https://www.virtualbox.org/manual/ch02.html#installation_windows
   • For Macs, detailed instructions can be found here: https://www.virtualbox.org/manual/ch02.html#idp46856129667856
   • For Linux, detailed instructions can be found here: https://www.virtualbox.org/manual/ch02.html#install-linux-host
2. Install the Ubuntu virtual machine (VM)
   1. Download Ubuntu_15.014_NBCR.ova: https://www.dropbox.com/s/qtzfxjldwxeu3la/Ubuntu_15.04_NBCR.ova?dl=0
   2. If the VirtualBox program is not running, open it by double clicking on the VirtualBox icon.
   3. Select “File” -> “Import appliance”
   4. Use the file dialog menu to select Ubuntu_15.014_NBCR.ova and click “Continue”
   5. If things have gone well, you should see something like the following:
      
   6. Click “Import” to install the virtual machine.