Class 7: Estimating Evolutionary Distance
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).Class 6: Alignment Algorithms
Project 2 Project 2 is now posted, and is due on Wednesday, 21 September, 8:59pm. Office Hours Update The location for Ashley’s office hours has moved to Olsson Hall 204. Other than the location, the office hours schedule is unchanged: Monday, 11am-noon: Jack (Rice 414) Monday, 1:30-2:45pm: Dave (Rice 507) Wednesday, noon-1pm: Ashley (Olsson 204) Wednesday, 2-3pm: Jack (Rice 414) Friday, 11:30am-12:30pm: Ashley (Olsson 204) Readings (Repeated from Class 5)Class 5: Analyzing Genomes
Readings Before Thursday, 8 September: Read Chapter 5 of the Bioinformatics Algorithms: How do we compare biological sequences?. Before next Tuesday, 13 September: Read Chapter 19 – 27 of Hubert’s The DNA Book. (Chapter 20 is a bit different, but may be useful to give you ideas for the kinds of things you could do for the Final Project.) Before next Thursday, 15 September: Chapter 26 of Manolis Kellis et al.Class 4: The Human Genome
Getting Email Notifications To get email notifications when there are posts in the Discussions site, you should select the “Watch” menu (upper right on https://github.com/computingbiology/fall2022) and select the notification you want. We recommend at least selecting from the “Custom” menu to get notifications for “Discussions” (if you want notifications for any updates, just select “All Activity”). Schedule and Readings Project 1 is due on Monday, September 5 (8:59pm). See the project for submission instructions.Class 3: Reading Genomes
Schedule and Readings Before Monday, 31 January: Read Chapter 11 – 18 of Hubert’s The DNA Book. Finish reading Chapter 3 (including 3.9) of the Bioinformatics Algorithms: How do we assemble genomes?. Project 1 is due on Monday, September 5 (8:59pm). Everyone should have a partner for Project 1, and be making progess on it. If you don’t have a partner for it, let Prof. Evans know. Slides The slides are here: Class 3: Reading GenomesOffice Hours
The office hours schedule has been updated:
Monday, 11am-noon: Jack (Rice 414)
Monday, 1:30-2:45pm: Dave (Rice 507)
Wednesday, noon-1pm: Ashley (Olsson 204)
Wednesday, 2-3pm: Jack (Rice 414)
Friday, 11:30am-12:30pm: Ashley (Olsson 204)
To schedule other times to meet with Dave use: https://davidevans.youcanbook.me/.
Class 2: The Platform for Life on Earth
Project 1 Project 1 is now posted, and is due on Monday, September 5 (8:59pm). Students will work in teams of two for Project 1, with constraints as discussed in Class 2: you can choose your partner or be assigned one “randomly” after class (today). If you choose your own partner, your team must satisfy these constraints: Both teammates went to different high schools Your answers to at least one of these questions must be different: What country were you born in?Class 1: Life
Schedule and Readings Before 8:59pm Wednesday 24 August: Read the Syllabus, Pledge, and complete the Registration Survey. After you submit the Registration Survey, you will receive an invitation (to the github account you include in your survey) to join the course github site (which will enable you to join the github discussions). Before Tuesday’s class, 30 August: Read Chapters 1 – 10 of Hubert’s The DNA Book (the chapters are very short and interesting, so its not as much as it sounds).Computer Science Background
Here is a guide to the computing theory background expected for students entering this course. If you’ve completed cs 2130 (Computer Systems and Organization 1) and a good Theory of Computation or Algorithms course (the official pre-requisites for this course) and remember the big ideas from that class, this should all be familiar to you already, but it may still be useful to refresh your understanding using these materials. If you haven’t taken the prerequisite courses and are getting up to speed on your own, we hope these materials will be helpful.Registration Survey
Everyone in the class should submit this course registration survey by Wednesday, 24 August at 7:59pm.