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BIOL/CMSC B115 Computing Through Biology: An Introduction¶

Spring 2016¶

General Information
Course Description
Tentative Schedule
Course Policies

General Information¶

Instructors¶

Joshua Shapiro joshua.shapiro@brynmawr.edu
Douglas Blank dblank@cs.brynmawr.edu

Meeting times and locations¶

Monday & Wednesday 2:40-4:00PM, Park 337
Open Lab: Thursday 9:00-11:00AM, Park 231

Office hours¶

Joshua Shapiro: Tuesday 9:30-11:00AM, and by appointment
Doug Blank: Monday & Tuesday 10:00-11:00AM, and by appointment

https://athena.brynmawr.edu/jupyter/

Course Description¶

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.

Learning objectives¶

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:

Read, write, and modify computer code in the Python language utilizing programming constructs such as variables, functions, loops, conditional statements, and objects.
Design, implement, and debug programs to perform computational tasks.
Understand the ideas behind computation, including the limits, requirements, and performance of different algorithms.
Model biological systems in a computational framework, and gain biological insights from those models in areas such as genetics, evolution, and ecology.
Understand common models of biological evolution and population genetics and explore their application to optimizing computational problems.

Textbook and Readings¶

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.

Readings on biological topics will be taken from a variety of sources, with all readings posted on the course website.

Tentative Schedule¶

Week	Date	Topic	Reading (Zelle)
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
13	Apr 11	Recursion
	Apr 13	Sequence alignment
14	Apr 18	Broader applications
	Apr 20	Project Presentations
15	Apr 25	Project Presentations
	Apr 27	Review for final

Course Policies¶

Assignments¶

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).

Computing¶

All computing will be done on the Athena cluster through your own computer's web browser. We will be using the Jupyter Notebook system with Python 3.

You can login to the Jupyter server at https://athena.brynmawr.edu/jupyter/. Accounts will be provided.

Exams¶

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.

Group project¶

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.

Grading¶

Final grades will be determined according to the following weightings:

40% Assignments
15% Exam 1
20% Exam 2
15% Group Project
10% Participation

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.

Support Services and Accommodations¶

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: (rheiser@brynmawr.edu, 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 (dalder@brynmawr.edu, 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.

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