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:
Leonard M. Adleman. Computing with DNA. Scientific American, August 1998.
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
James Bornholt, Randolph Lopez, Douglas M. Carmean, Luis Ceze, Georg Seelig, Karin Strauss. A DNA-Based Archival Storage System, ASPLOS 2016.
Bichlien H. Nguyen, Christopher N. Takahashi, Gagan Gupta, Jake A. Smith, Richard Rouse, Paul Berndt, Sergey Yekhanin, David P. Ward, Siena D. Ang, Patrick Garvan, Hsing-Yeh Parker, Rob Carlson, Douglas Carmean, Luis Ceze, Karin Strauss. Scaling DNA data storage with nanoscale electrode wells, Science Advances, 24 November 2021.
Brian J. Cafferty, Alexei S. Ten, Michael J. Fink, Scott Morey, Daniel J. Preston, Milan Mrksich, and George M. Whitesides. Storage of Information Using Small Organic Molecules, ACS (American Chemical Society) Central Science, May 2019.
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.
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.
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.
