Syllabus

  • The class will meet Mon and Wed at 9 am 1 hr, and then Fri for 2 hr.

  • Because of COVID-19, all class time and office hours will be done via zoom. The class will meet remotely at the times above.

  • All communication about the class will be done via slack.

People

  • Mike Harms (professor)

  • Luis Perez (TA)

  • Joseph Harman (volunteer TA)

  • Anneliese Morrison (volunteer TA)

  • Michael Shavlik (volunteer TA)

Conceptual Goals

By the end of the course, students should understand:

  • Basic python: data types, key words, control, functions and imports

  • Core python extensions for scientists: scipy, numpy, matplotlib, and jupyter

  • Strategies for dissecting problems and formulating solutions in code

  • Where to go to pick up skills in the future as the need arises

Skill Goals

By the end of the course, students should be able to:

  • Write basic python programs from scratch

  • Identify existing libraries for a problem and learn how to use them

  • Generate arbitrarily complex custom plots

  • Simulate experimental sampling

  • Manipulate scientific datasets of the following types (at a basic level):

  • High-throughput sequencing data

  • Chemical structure data from databases such as the PDB

  • Images

Course schedule

Assignments

All assignments should be turned in on canvas. Assignments are due by 9 am on the day they are due.

Final project

  • Project prospectus (Due Friday, May 8)

  • Final project (Due Monday, June 9)

  • The descriptions of these assignments, as well as the grading rubric, are given in the Final project description.

Weekly assignments

  • There will be 8 labs.

  • We will (generally) start the labs on Fri in class.

  • They will (usually) be due the following Wed in class.

  • Please compress the entire folder containing your jupyter notebook and associated input files. This will make sure we can run the notebook when grading.

  • Labs will be graded based on whether they are turned in, whether we can run the notebook, and whether they notebooks give the right results.

  • Group work on the labs is encouraged, but please do not copy-paste code.

Grading

Assignment

Point %

units points

num assignments

total points

Attendance

25 %

6 pts/class

30 classes

180

Labs

50 %

45 pts/lab

8 labs

360

Proposal

2.5 %

18 pts

1

18

Final project

22.5 %

162 pts

1

162

Total

720

  • The points posted on Canvas are the offical point totals. If you think there has been a mistake with your points, please contact me.

  • Anyone receiving 90% or more of the points will receive an A, 80%-90% a B, etc. I may curve the course, but this will only improve your grade from the baseline above.

Community

This class is governed by the UO community standards.

  • Respect the dignity and essential worth of all individuals.

  • Promote a culture of respect.

  • Respect the privacy, property, and freedom of others.

  • Reject bigotry, discrimination, violence, or intimidation of any kind.

  • Practice personal and academic integrity and expect it from others.

Students with Disabilities

If you have a documented disability and anticipate needing accommodations in this course, please make arrangements to meet with Mike soon. Please bring a notification letter from the Accessible Education Center (http://aec.uoregon.edu/) outlining your approved accomodations. In particular, if remote-learning will be an issue, please let me know as soon as possible so I can work with you.

Cheating

TL;DR: Don’t do it. You are expected to do your own work. Cheating, plagiarism and any other form of academic dishonesty will not be tolerated. Please refer to the University of Oregon Student Conduct Code (https://policies.uoregon.edu/vol-3-administration-student-affairs/ch-1-conduct/student-conduct-code).

Auditors

If you are not taking the course for credit:

  • Please come to a session you RSVP for. If you are not coming, please let me know 24 hours in advance so I can plan the groups accordingly.

  • You should do all in-class work as though you are in class. You are welcome to complete the assignments and turn them in for feedback. (If time becomes limiting, I may have to revisit this policy.)

  • I am happy to work with you to do a final project.