This is the page in which I try to be somewhat organized with information for summer students :).

Every Week

The structure on a typical week will be:

  • One-on-one meeting with Anya ~30 minutes
  • Daily group ‘stand-up’ meeting ~15 minutes
  • Weekly longer group meeting ~1 hour
  • Expectation that you work 40 hours and make the meetings but otherwise schedule is flexible
  • You are encouraged to work in our room, Olin 312, but not required
  • You are encouraged to ask each other for help and advice first and help each other when asked, though always also welcome to get help from me

June 21st

Group meeting at 10:30am

We’ll have initial group meeting at 10:30am in our meeting room, Olin 312, which is on the third floor of Olin.

At that meeting we’ll discuss:

  • Anya’s schedule this week (it’s busy)
  • Introductions and expectations
  • The two main projects
  • RCR training (see below)
  • When the group meetings will be

RCR (Responsible and Ethical Conduct of Research)

Many federal grant making agencies – including the National Science Foundation and the National Institutes of Health – require grantees like me to prove that they provide appropriate training and oversight for all researchers on a project in the responsible and ethical conduct of research (RCR).

To meet these requirements, Carleton has subscribed to Collaborative Institutional Training Initiative (CITI) to provide “RCR for Undergraduate Researchers” that can be used by anyone involved in a federal grant to obtain RCR training, including but not limited to research trainees such as undergraduates. If you have already completed RCR training as an undergraduate, you need not do so again.

The step-by-step instructions to access the CITI training modules are provided on the College’s Responsible Conduct of Research page. The training includes 6 required modules and 3 elective modules.

These quizzes must be completed by June 21. Once you complete the quizzes, I will be notified.

Rest of Week 1

Project preferences

You should email or Slack message me what your preferences are for project and partner or that you don’t have a preference.


You should read the PDF I post to Slack with the review on symbiosis in digital evolution both for your own understanding of the field and take notes of any typos or confusing parts and let me know (it’s a work in progress!).

If you have extra time, you can read the many references in that review based on what interests you.

Computer Setup

You’ll be running experiments on my two research servers which only support ssh. Verify that you can log on to both (though you’ll probably only use one, we’ll divide them by project):


(Curious about the names? Read about John Edmonstone and Lynn Margulis)

I recommend you use VSCode for working with the code base locally, though it’s not required. We’ll use git to share code and move it between your local machine and the research servers, so if you aren’t familiar with git and GitHub or would like a refresher, look through this guide. I also recommend RStudio for when you eventually want to make plots/graphs, so you can download that right away (the free version!).


We’ll be making additions to my software, Symbulation, so download it (with git) from here along with Empirical and try running it. Explore the different settings in SymSettings.cfg and try changing them to see what happens!

Getting Started

I’ll let you know which project you’re working on and with whom ASAP, at which point you two can meet and start planning first steps to work toward the goal!

Handy Commands

(Anya forgets about these and so this is somewhat a reminder for them but also useful for students)

To see the load on the cores on the servers:


To get C++17 working on the servers, run:

scl enable devtoolset-9 bash

To run a process in the background:

screen python stats_scripts/

Use the key sequence Ctrl-a + Ctrl-d to detach from the screen session. At this point you could close the window or go do other things while this is running.

To reattach, on the command prompt type

screen -r