Scholar's Backpack

Modern research practice asks researchers to engage with information in new ways through the use of a rapidly changing array of digital technologies. The Scholar’s Backpack brings together a sampler of commonly used scientific computing tools into one virtual machine, both decreasing the overhead of locating, installing, and learning how to use new tools and improving the reproducibility of scientific computing environments.

Getting Started

1. Install VirtualBox and Vagrant.

   • Vagrant 2.0 or higher is required.
   • Windows users must also install a shell environment like Git for Windows.

2. Clone or download this repository as a zip file.

3. From a terminal application, navigate to the scholars-backpack directory, type vagrant up, and hit the Return key.

4. Once Vagrant is finished, type vagrant ssh to access the virtual environment. This environment has been configured to automatically change the directory to /vagrant/code on the guest machine.

Running the Introductory Jupyter Notebook

Jupyter notebooks are accessible from localhost:5453

R Studio

R Studio is accessible from localhost:5452

Username: vagrant

Password: vagrant

What's inside?

Python

This environment uses Anaconda 5.0.1 to install and manage Python. A complete list of included packages can be found under the Python 3.6 package list.

R

Anaconda is also used to manage R. This environment uses the conda package r-essentials. The default R working directory is automatically configured to /vagrant/code.

The following additional R packages are installed using conda:

• plotly

Vagrant Notes

• To exit the guest environment, type exit from the command line anywhere in the guest.
• To shut down the virtual machine, type vagrant halt from within the scholars-backpack directory on the host.
• To turn on the virtual machine, type vagrant up from within the scholars-backpack directory on the host.
• For more detailed information, visit the Vagrant Documentation