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:
- Leonard M. Adleman. Computing with DNA. Scientific American, August 1998.
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:
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George M. Church, Yuan Gao, and Sriram Kosuri. Next-Generation Digital Information Storage in DNA (and Supplemental Materials with the code and details!), Science, August 2012.
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Here’s the 3Blue1Brown video on error-correcting codes: How to send a self-correcting message (Hamming codes)
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William H. Press, John A. Hawkins, Stephen K. Jones, Jeffrey M. Schaubd, and Ilya J. Finkelsteind. HEDGES error-correcting code for DNA storage corrects indels and allows sequence constraints. PNAS, August 2020.
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Jacques Bonnet, Marthe Colotte, Delphine Coudy, Vincent Couallier, Joseph Portier, Bénédicte Morin, Sophie Tuffet. Chain and conformation stability of solid-state DNA: implications for room temperature storage. Nucleic Acids Research, March 2010.
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James Bornholt, Randolph Lopez, Douglas M. Carmean, Luis Ceze, Georg Seelig, Karin Strauss. A DNA-Based Archival Storage System, ASPLOS 2016.
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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.
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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.