Course materials

Monday, November 29th

Homework due: Work through mapping short reads to the Campylobacter genome with bowtie, and try out various parameters with bowtie. Choose your favorite set of parameters (with a brief explanation of why they're your favorite), generate the positional variation plot, and send them to Titus and Heather. Please do this well before class on Monday, thanks!

Friday, November 12th

Homework due: Avida project due! Please write up a 2-3 page report, in PDF, on your avida project, or prepare a 5 minute presentation (and let us know if you are going to present). Either the report or the presentation should cover the following topics:

  1. What you wanted to analyze or discover from this project;
  2. Experimental setup, with some detail on your configuration;
  3. Results;
  4. Questions, comments, or thoughts on how to set up a better experiment next time;
  5. What you would want to do next were you to continue working on this project.

Monday, November 1st

Homework due: Use the mutation analysis (see also this tutorial) scripts to do a point-mutation analysis of either the starting organism or an evolved organism. Send in the plots as PDFs, along with the organism source genome, to Titus and Heather.

Monday, October 25th

Friday, October 22nd

Lecture 14: the git version control system [ PDF ]

Monday, October 18th

Work through the running serial transfers tutorial and spend some quality time with the script, which does all the heavy lifting. Can you run your proposed experiment with this? (If so, try it out!) If not, what additional scripts or capabilities do you need? If you need something more, talk to Heather and Titus.

Lecture 13: Version control etc. [ PDF ]

Friday, October 15th

Medium homework DUE: Revisit your proposed project and identify (a) what kind of configuration files you'll start with, (b) what kind of serial transfer you'll want to do (if any), (c) any systematic changes you'll want to make to the configuration files during the transfer, and (d) what kind of measurements you want to make. Break (a-c) down into a computational pipeline for doing your project, and send it to Heather and Titus (again ;).

Monday, October 10th

Lecture 11 - Configuring Avida [ PDF ]

Light homework DUE: Alone or in a small group, write up a paragraph or so with ideas for a Not-So-Long-Term Evolution Experiment with Avida a la Lenski & Travisano. Send to Titus and Heather before class. Having a hypothesis is good but not necessary.

See Lecture 10 materials (Fri, Oct 8th) for inspiration; you can also listen to a recent MicrobeWorld podcast, Meet the Scientist: Charles Ofria.

Friday, October 8th

Lecture 10 - LTEE, and Fitness Landscapes [ PDF ]

Reading: Dynamics of adaptation and diversification (Lenski and Travisano, PNAS, 1994)

Monday, October 4th

Lecture 9 - Making Sense of Data [ PDF ]

Friday, October 1st

Assignment: critter-off! Evolve a critter under whatever mutation rate you want, and send it to us to battle in a gladitorial arena! After setting the mutation rate in avida.cfg (see: COPY_MUT_PROB), follow these instructions to retrieve the dominant organism. Take this entire last line and copy/paste it into an e-mail to Titus ( and Heather ( Due Friday, October 1st.

Lecture 8 - Scripting Pipelines [ PDF ]

Suggestion -- keep your mutation rate under 2.5%...

Monday, September 27th

Lecture 7 - On Scripting [ PDF ]

Friday, September 24th

Lecture 6 - Replication vs Reproduction [ PDF ]

Assignment: Before class, read the two papers sent out via the mailing list ("The Trouble with Replication" and "The evolutionary origin of complex features" [ PDF ].

Monday, September 20th

Lecture 5 - On computing [ PDF ].

Friday, September 17th

Assignment: follow the instructions for installing and running avida, and then copy and paste the *last line* from running avida and send it in an e-mail to the entire class at The line should look something like this:
UD: 500     Gen: 38.63245   Fit: 0.2491669  Merit: 96.38030   ...
but yours may differ. If you are working together, make sure you each individually run avida and send the results out.

Note, there are a number of reasons you should not leave doing this HW to the last minute...

Monday, September 13th

Lecture 3 - Intro to Avida (with movies!)

Friday, September 10th

Assignment: Sign up for an account at and enable it for EC2 (Elastic Cloud Computing). (If you already have an account, you still need to sign up for AWS, but the account information will otherwise be the same.)


  1. Go to
  2. Sign up for an account.
  3. Log into the account.
  4. Click on the "Amazon EC2" tab at the top.
  5. Click the "Sign Up for Amazon EC2" button and follow the instructions.
If you don't have to provide a credit card number and receive a phone call, you have not successfully signed in!

You will need this to do your homework for the following Friday. (We will provide you with a code to pay for the first $100 of computer usage, which should be enough for the entire course.)

Friday, September 3rd

Lecture 1, Introduction (PDF) - (pptx)

Index page for CSE 891 / Computational Science...

Lab of Genomics, Evolution and Development /