Monday, November 29th
Homework due: Work
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:
- What you wanted to analyze or discover from this project;
- Experimental setup, with some detail on your configuration;
- Questions, comments, or thoughts on how to set up a better experiment
- What you would want to do next were you to continue working on this
Monday, November 1st
(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
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
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
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),
to retrieve the dominant organism. Take this entire
last line and copy/paste it into an e-mail to Titus (email@example.com) and
Heather (firstname.lastname@example.org). 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
Monday, September 20th
Lecture 5 - On computing
[ PDF ].
Friday, September 17th
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 email@example.com
. 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
Sign up for an account at aws.amazon.com
and enable it for EC2 (Elastic Cloud Computing). (If you already have an amazon.com account, you still need to sign up for AWS, but the account information will otherwise be the same.)
- Go to aws.amazon.com.
- Sign up for an account.
- Log into the account.
- Click on the "Amazon EC2" tab at the top.
- 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)