You can download the syllabus here. The syllabus includes information on grading, course goals, and policies I will use in teaching this course.
We will be using Python for Biologists and Advanced Python for Biologists, by Martin Jones. These books were written especially for scientists who are new to programming. The author maintains a website for the books here.
Specific assignments are given below. Please note that homeworks are very important, and make up a very large portion of your grade. If you fall behind, you will likely do poorly on the exams as well. Homework should follow the specifications given here.
Homeworks can be turned in here.
Additional resources will be placed here.
Click here if you’re in the class, for more useful information.
This is a tentative schedule for the class. I may change it depending on how the class progresses.
Reading | Subject | Homework | Due Date | Files | |
---|---|---|---|---|---|
1 | PfB 1-2 | Basic Text | DNA Strings | January 26 | dna_strings.ipynb |
2 | PfB 3 | Reading & Writing Files | Chemical Database | January 31 | — |
3 | PfB 4 | Lists & Loops | FASTA files | February 5 | elephant.fasta |
4 | PfB 5 | Functions | Unicorn Genetics | February 12 | male-unicorns.gene female-unicorns.gene |
Midterm 1 | |||||
5 | PfB 6 | Conditionals | River pH | February 26 | river-pH.tsv |
6 | PfB 7 | Regular Expressions | Kraken Genetics | March 8 | kraken.gene |
Spring Break! | |||||
7 | PfB 8 | Dictionaries | Molecular Weight | March 22 | element-weights.tsv |
8 | APfB 1-2 | Recursion & Trees | Clades of Spiders | March 29 | spiders.tree |
Midterm 2 | |||||
9 | APfB 3 | Tuples, Sets & Lists of Lists | Draconic Parsimony | April 12 | dragons.gene |
10 | APfB 4 | Classes | Elemental Encyclopedia | April 19 | elements.tsv |
11 | — | Classes | DNA, RNA & Polypeptide Objects | April 26 | genetic-code.tsv |
12 | APfB 7 | Exceptions | Open Project | May 3 | — |
Final Exam: Friday May 12, 12:00 |