This is an archived file from the Spring 2022 version of the course.
See the current course website for a more recent version.

Fall 2022 Course

This course will be offered again in in Fall 2022. The course will be somewhat similar to the Spring 2022 course (which you can explore here, including the Syllabus and Schedule, but with some changes based on what we learned last spring and new versions of these will be posted soon.

The Fall 2022 course is scheduled for Tuesdays and Thursdays, 12:30-1:45pm in Olsson Hall 120.

Final Projects

Here are final projects with public websites available. Meghan Anderson, Kathia Crawford, Izzy Shehan, Visualizing and Understanding Olfaction [Github Repo] Presentation Jason Calem, Will Pemble, Gabriel Silliman, Cooper Scher, DNA Profiling with Incomplete Databases Presentation Yanjin Chen, Gene network analysis Marvin Cheng, Computer Vision and Human Vision Github Brenna Courtney, On Christian Bök’s The Xenotext (Book 1) Wikipedia Page Colin Crowe, The Mystery of Chargaff’s Second Parity Rule Presentation)

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Final Project Presentations

Wednesday, 27 April

Monday, 2 May

Project Presentations Schedule

Project Presentations Each team will have an opportunity to present your project to the class on either Wednesday, 27 April or Monday, 2 May. You will have 5 minutes maximum for your presentation (which will need to be enforced strictly to be able to complete all the presentations within the schedule class period). It is fine if your presentation is shorter (which might even allow time for questions), but you should keep the time limit in mind in planning your presentation.

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Class 25: Computational Biology: Ensembles of Trees (Guest: Kristen Naegle)

Slides

Our guest speaker today was Kristen Naegle, Professor of Biomedical Engineering. Her slides are here: Computational Biology: Ensembles of Trees.

Class 24: Protein Folding and AlphaFold

Schedule Project Update: due tomorrow, Tuesday, 19 April, 4:59pm. Submission Form Slides Slides: class24.pdf Links Ken A. Dill, S. Banu Ozkan, M. Scott Shell, and Thomas R. Weikl. The Protein Folding Problem. Annual Review of Biophysics, 2008. Bonnie Berger and Tom Leighton. Protein Folding in the Hydrophobic-Hydrophilic Model is NP-Complete. RECOMB 1998. Scott Aaronson, NP-complete Problems and Physical Reality. Andrew W.

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Class 23: Programmable Pharmacueticals

Schedule Project Update: due Tuesday, 19 April, 4:59pm. An update on how your project is going, any changes from your original plans, and summary of what progress you have been able to make. (A link to a form for submitting this will be posted on April 18.) Slides Slides: class23.pdf Causes of Death There was a great question about what fraction of all deaths are accounted for in the statistics I showed from Our World In Data.

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Class 22: Implementing DNA Storage

Schedule Project Update: due Tuesday, 19 April, 4:59pm. An update on how your project is going, any changes from your original plans, and summary of what progress you have been able to make. (A link to a form for submitting this will be posted on April 18.) Slides Slides: class22.pdf Links 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.

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Class 21: DNA Storage

Schedule Project Proposal (see Final Project for details) is due Friday, 8 April (7:59pm). Use this form to submit your project proposal (which is just a PDF file): Project Proposal Form. Slides Slides: class21.pdf Links Here’s the 3Blue1Brown video on error-correcting codes: How to send a self-correcting message (Hamming codes) Catherine Taylor Clelland, Viviana Risca, and Carter Bancroft. Hiding messages in DNA microdots. Nature, June 1999.

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Class 20: Membrane Computing

Schedule Project Proposal (see Final Project for details) is due Friday, 8 April (7:59pm), except for teams on the early schedule when it is due Today, Monday, 4 April (7:59pm). Use this form to submit your project proposal (which is just a PDF file): Project Proposal Form. Slides Slides: class20.pdf Links S. J. Singer and Garth L. Nicolson. The Fluid Mosaic Model of the Structure of Cell Membranes. Science, Febriary 1972.

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