There will be periodic computer-based activities that might require software installations on your computers. All of these are open-source (free) and routinely used in science (safe). If you are ever confused, stop and ask for help. Activities are meant to reinforce concepts covered in class; manipulating models or simulating evolution yourself should make the intended learning goals more tangible. The reason for having these tools on your own computer is to create opportunities for inquiry beyond scheduled meeting times. I do not recommend anybody install something that I have not personally used or used in a teaching environment before.

Prior experience using command line programs or programming in general can be helpful but is not necessary. Some exercises will be woven into class content or into assignments, and these help develop foundational skills for approaching evolutionary biology research. Additional office hours will be created in advance of computational assignments to help ensure everyone is prepared and has a positive experience with class activities.

Some common prerequisites

If you do not already have them, please install the following:

  • install R and R Studio
  • install a text editor for editing or writing code if you do not already have one. I strongly suggest VSCode as well as a simpler plain text editor with fewer features:
    • VSCode for all systems but with some extra features for coding
    • BBEdit for Mac users
    • Notepad++ for Windows users
  • install Python
    • there are now many ways to install Python and its associated package managers. If this is your first time installing Python, my honest opinion is that you want to install the version distributed through miniconda. This will not only put Python in the right place for you, but also install many of the packages that other Python packages depend on.
    • Please note that Anaconda Foundation products (including miniconda) have a terms of use agreement. It is free for you as an individual and for education and research. If you also work for a company or government agency with more than 500 employees, you should avoid using miniconda and other Anaconda products so as not to violate the terms of use. Come talk to me if this is you.

For Windows users

  • install Git for Windows
    • This provides a UNIX-like environment on your Windows machine. It will ensure everyone is on the same page for activities rather than having branching paths for Windows and UNIX-based users.