Class 11

Final Project

The first deliverable for the Final Project is the Project Team and Idea Form, which we discussed in class today. It is due tomorrow, Friday, 30 September (AoE). See the Final Project Page for more information on the final project.

Reading Assignment

October 3 – 4 are Fall “Reading Days”. I will be out of town and not have my usual office hours on October 3. Your reading assignment (to complete before our next class on Thursday, October 6) is this paper on computing with DNA:

An additional (optional) reading is an earlier, slightly more technical, paper on the same experiment: Leonard Adleman, Molecular Computation of Solutions to Combinatorial Problems, Science, November 1994.

We will talk about these in next Thursday’s class, but please post any questions or thoughts you have on them in the Discussions.

Quiz

We’ll have our first quiz in class on Tuesday, 11 October (as scheduled on the syllabus). (If you are unable to make it to class on October 11, let me know in advance and there will be an alternate way to take the quiz.)

This and subsequent quizzes are not meant to be stressful and something that will adversely impact grades for students who are doing well, but are intented to provide “polite” nudges to encourage students to do the readings and be engaged in classes, and to think about and lightly review things we have done so far.

It will have questions (most of which will expect short answers) on:

  • Big concepts in biology from classes + readings so far
  • Main ideas in this week’s classes
  • The assigned Adleman paper (above) and what we do in class next Thursday

Slides

The slides are here: Class 11: Implementing DNA Storage

Some links to materials for the class:


Class 10

Project 2

Project 2 is due tomorrow (Wednesday, 28 September) at 8:59pm.

Final Project

The first deliverable for the Final Project is the Project Team and Idea Form, which we discussed in class today. It is due Friday, 30 September (AoE). See the Final Project Page for more information on the final project.

Slides

The slides are here: Class 10: DNA Storage

Some links to materials for the class:


Class 9

Project 2

Project 2 is now due Wednesday, 28 September, 8:59pm.

Final Project

The first deliverable for the Final Project is due Friday, 30 September, 8:59pm. This is just a form submission to provide your team and idea for the final project, or other information if you need help to find a team or idea.

Slides

The slides are here: Class 9: Distance-Based Phylogeny

Some links to materials for the class:


Class 8

Project 2

The deadline for Project 2 has been extended to Monday, 26 September, 8:59pm.

Readings

See Class 5 for this week’s readings.

Slides

The slides are here: Class 8: Phylogeny

Some links to materials for the class:


Class 7

Project 2

Project 2 is now posted, and is due on Wednesday, 21 September, 8:59pm.

Correction to Alignment Code! As was noticed in class today, the code for the gap-based alignment algorithms is wrong. The loops should include all values up to and including j (so should be

range(1, j + 1)

instead of

range(1, j)

(note that range in Python iterates through the values from the first input up to, but not including, the second input value, so to include j in the iteration, we need to use j + 1 in the range).

Thanks to Diego Wang for submitting this pull request with the fix and explanation.

If you have already modified your Project 2 notebook (which hopefully is true for everyone!), you should incorporate the change manually into the code in your notebook to avoid losing the work you have done.

Readings

See Class 5 for this week’s readings.

Slides

The slides are here: Class 7: Estimating Evolutionary Distance

Some links to materials for the class: