Monday & Wednesday 2:40-4:00PM, Park 337
Open Lab: Thursday 9:00-11:00AM, Park 231
Joshua Shapiro: Tuesday 9:30-11:00AM, and by appointment
Doug Blank: Monday & Tuesday 10:00-11:00AM, and by appointment
This course is an introduction to biology through computer science, or an introduction to computer science through biology. The course will examine biological systems through the use of computer science, exploring concepts and solving problems from bioinformatics, evolution, ecology, and molecular biology through the practice of writing and modifying code in the Python programming language. The course will introduce students to the subject matter and branches of computer science as an academic discipline, and the nature, development, coding, testing, documenting and analysis of the efficiency and limitations of algorithms.
The goal of this course is to introduce concepts from computer science and biology in an integrated approach, while drawing connections between these two fields of study. Specifically, students completing the course should be able to:
For the computer science topics of the course, we will be using Python Programming, Second Edition by John Zelle. Be sure to get the second edition, as it covers Python 3, which is the version of the language that we will be using.
<img src="http://mcsp.wartburg.edu/zelle/python/ppics2/cover.png" alt= "Python Programming, second edition cover image" style="display: block; margin-left: auto; margin-right: auto">
Readings on biological topics will be taken from a variety of sources, with all readings posted on the course website.
|1||Jan 20||Modeling life through simulations||Chapter 1|
|2||Jan 26||Simple programs - Python simulation||Chapter 2, 7.1-7.3|
|Jan 28||Stochastic simulation, Random & pseudorandom numbers|
|3||Feb 1||DNA sequence analysis: GC content - math, strings, functions||Chapter 3, 5.1-5.2, 6|
|Feb 3||GC content variation across genomes & species - lists, graphics||Chapter 4, 11.1-11.3|
|4||Feb 8||DNA Translation - files, dictionaries||Chapter 5.3-5.10, 11.1-11.3, 11.6|
|Feb 10||Debugging & testing|
|5||Feb 14||DNA mutations, types & effects - modular arithmetic||Chapter 7|
|Feb 16||Sorting & analysis|
|6||Feb 22||Evolving digital organisms|
|Feb 24||Evolving digital organisms|
|7||Feb 29||Review for exam|
|Mar 2||Exam I|
|8||Mar 7||Spring Break|
|9||Mar 14||Population genetics: Random Genetic Drift - arrays, random||Chapter 8|
|Mar 16||Genetic drift with mutations: infinite vs finite sites - program design||Chapter 9|
|10||Mar 21||Haploids, diploids & mating - classes & objects||Chapter 10|
|Mar 23||Additivity & dominance in evolution|
|11||Mar 28||Project Brainstorming & Design|
|Mar 30||Learning Systems & Plasticity|
|12||Apr 4||Training a neural network|
|Apr 6||Algorithm design & efficiency||Chapter 13|
|Apr 13||Sequence alignment|
|14||Apr 18||Broader applications|
|Apr 20||Project Presentations|
|15||Apr 25||Project Presentations|
|Apr 27||Review for final|
There will be approximately ten assignments, consisting of programming problems and explorations of biological questions through computational approaches. Assignments will be submitted through Jupyter (below).
You can login to the Jupyter server at https://athena.brynmawr.edu/jupyter/. Accounts will be provided.
There will be two exams in the course, one mid-semester and the other during finals period. The exams will cover material from lectures, homeworks, and assigned readings (including topics not discussed in class). Both exams will be closed-book and closed-notes.
During the second half of the semester, students will work in small (2-3 person) groups on an independent programming project that explores an area of biology through computation. Topics may include simulations of genetic regulatory systems, modeling of population dynamics or epidemiology, bioinformatic data analysis, or any other topic of interest in biology. Groups will present their work in an oral presentation to the class, and through a Jupyter notebook that clearly describes both the biological questions being addressed and the computational approaches taken.
Final grades will be determined according to the following weightings:
15% Exam 1
20% Exam 2
15% Group Project
Late assignments will incur a 10% penalty per day unless arrangements are made for an extension at least 24 hours prior to the due date. Extensions will only be granted in the case of verifiable medical excuses or other similarly dire circumstances. All exams and projects are required; failure to complete any component will result in failure in the course.
Bryn Mawr offers a variety of resources to help students thrive in their academic endeavors while managing stress and maintaining mental health. For further information on those services, consult the Support Services website or contact Rachel Heiser, Academic Support and Learning Resources Specialist in the Dean’s Office, with questions: (firstname.lastname@example.org, 610-526-5275)
Students who think they may need accommodations in this course due to the impact of a learning, physical, or psychological disability are encouraged to meet with me privately early in the semester to discuss their concerns. Students should also contact Deb Alder, Student Access Coordinator (email@example.com, 610–526–7351), as soon as possible, to verify their eligibility for reasonable academic accommodations. Early contact will help to avoid unnecessary inconvenience and delays.