CS21B — Intro to Comp Sci: Apps in Biology
Spring 2011

Schedule | Lab Sessions | Study Sessions | Succeeding | Grading


The study guide for the final exam is available. The final is scheduled for Saturday, May 7th 2-5pm in SCI 101.

Class Information

Class: Tuesday, Thursday 9:55–11:10am, SCI 240
Lab: Friday 2:00–3:30pm, SCI 256
Professor: Lisa Meeden
Office: SCI 243
Phone: 8565
Office hours: I will be available Wednesdays 2-4pm, or you can stop by whenever my door is open.

Welcome to CS21B. This course will introduce fundamental ideas in computer science and teach you how to write computer programs while exposing you to some applications in biology. We will study algorithms for solving problems and implement solutions in the Python programming language. Python is an interpreted language that is known for its ease of use. We also introduce object-oriented programming and data structures. A deeper coverage of these topics is presented in CS 35.

This course is appropriate for all students who want to learn how to write computer programs and think like computer scientists. It is also one of the usual first courses for computer science majors and minors. Students with advanced placement credit or extensive programming experience should place out of this course and instead begin with CS33 or CS35.

Comments from former students

Kaz Uyehara, Biology Major '10
This class was a a great opportunity to learn a programming language and actively connect programming with biological topics. Computer programs are now a necessity in many fields of biology and this introductory class has given me the background to understand when a well written program could make certain tasks more efficient, how to tweak existing programs to my specific needs, and how to solve problems by creating my own programs. I am already thinking about using python programs in the 9th grade science course that I teach and even in my biodiversity research.

Seth Donoughe, Biology Major '08
I wish I had taken more CS classes at Swat when I had the chance, but even what I learned in the intro class has proven to be really useful. I've been able to write python programs designed specifically to help me to transform and analyze data that I gather in experiments, in the process saving me from loads of tedious work and enabling me to be more creative in how I extract meaningful results from big datasets. On a broader level, learning the basics of how to program has been quite helpful in two ways. 1) I can apply it to other areas with simple languages (e.g. writing macros for ImageJ or Excel --- both of which are very commonly used in bio labs), and 2) Now I'm no longer utterly bewildered and intimidated when it comes to programming --- meaning that picking up a new programming language at least seems plausible.

Required Textbook

Goals for the course

By the end of the course, we hope that you will have developed the following skills:

Student Support

Student Support Coordinator: Betsy Horner (Office: Science Center 257, Phone: 6062)

Ninjas (student mentors): Jonathan Gluck and Frank Chien will be specifically assigned to our class (CS21B) and will be most able to help you with our labs. Other ninjas, helping with all sections of CS21, include: Ashley Oudenne, Haley Most, Brandon Snuggs, Amanda Morrison, Emily Dolson, and Josh Bloom. These student mentors can help explain general programming concepts and assist you in studying for quizzes.

Study sessions

The CS Ninjas will assist me in class and run study sessions on the following evenings:

Day Time Location
Sunday 7-9pm For CS21B
Sci Center 256
Wednesday 7-9pm Sci Center 240

You are invited -- and encouraged -- to participate in these study sessions to prepare for quizzes, to discuss programming concepts, and to get friendly assistance in working on homework assignments. Our CS mentoring team is dedicated to helping students, who have no prior knowledge of computer science, learn to program in Python while keeping their senses of humor intact. As an added bonus, free food will be provided at the sessions.

Lab Session

CS21B will have a lab session every Friday in SCI 256 from 2:00-3:30. You are required to attend this lab section. Please contact me in advance if you are unable to attend lab.

In addition, the CS lab (SCI 240) is open 24 hours a day, 7 days a week for you to use to work on your lab assignments.

Accessing the CS labs after hours

You can use your ID to gain access to SCI 238 or SCI 240 at nights and on the weekends. Just wave your ID over the microprox reader next to the lab doors. When the green light goes on, just push on the door handle to get in (the door knob will not turn). If the green light doesn't go on, then we need to enter your microprox number into the system. email local-staff@cs.swarthmore.edu if you have problems with this. If the building is locked, you can use your ID to enter the door between Martin and Cornell library.

How to succeed in this class

Academic Accommodations

Academic accommodations are available for students with disabilities who are registered with Student Disability Services in the Dean's office. Students in need of disability accommodations should schedule an appointment with me early in the semester to discuss accommodations for this course that have been approved by the Dean's office. All requests must come through an accommodation letter from the Dean's office. To receive an accommodation for a course activity, your meeting with me must be at least one week prior to the activity.

Contact Tracey Rush at the Dean's office and follow these steps for obtaining accommodations.


Grades will be weighted as follows:
40%Homework assignments
30%Quizzes (there will be 6 quizzes, see schedule for dates)
5%Class Participation
25%Final Exam

Homework policy

Programming assignments will be introduced in lab on Fridays and will be due before midnight the following Tuesday night. You are strongly encouraged to start early and to attend the study sessions for extra practice.

You will submit you assignments electronically using the handin21b program. You may submit your assignment multiple times, but each submission overwrites the previous one and only the final submission will be graded. Late assignments will not be accepted except in extreme situations and only if you contact me before the deadline. Even if you do not fully complete an assignment, you should submit what you have done to receive partial credit.

Programming Style

Programming is not a dry mechanical process, but a form of art. Well written code has an aesthetic appeal while poor form can make other programmers and instructors cringe. Programming assignments will be graded based on style and correctness. Good programming practices usually include many of the following principles:

Academic Integrity

Academic honesty is required in all work you submit to be graded. With the exception of your lab partner on lab assignments, you may not submit work done with (or by) someone else, or examine or use work done by others to complete your own work. Your code should never be shared with anyone; you may not examine or use code belonging to someone else, nor may you let anyone else look at or make a copy of your code. This includes sharing solutions after the due date of the assignment.

All code you submit must be your own with the following permissible exceptions: code distributed in class, code found in the course text book, and code worked on with an assigned partner. In these cases, you should always include detailed comments that indicates on which parts of the assignment you received help, and what your sources were.

Discussing ideas and approaches to problems with others on a general level is fine (in fact, we encourage you to discuss general strategies with each other), but you should never read anyone else's code or let anyone else read your code. You may discuss assignment specifications and requirements with others in the class to be sure you understand the problem. In addition, you are allowed to work with others to help learn the course material. However, with the exception of your lab partner, you may not work with others on your assignments in any capacity.

``It is the opinion of the faculty that for an intentional first offense, failure in the course is normally appropriate. Suspension for a semester or deprivation of the degree in that year may also be appropriate when warranted by the seriousness of the offense.'' - Swarthmore College Bulletin (2008-2009, Section 7.1.2)

Please see me if there are any questions about what is permissible.


1 Jan 18   Intro to Python and Unix
Zelle chapters 1-2
Notes on Using Emacs
Lab0: Unix & Emacs
Lab1: First Programs
Jan 20  
2 Jan 25   Numbers and Strings
Zelle chapters 3-4
Lab2: Translation
Jan 27 Quiz 1
Quiz 1 Study Guide
Drop/Add ends (Jan 28)
3 Feb 01   Booleans
Zelle chapter 7 and pg. 247
Lab3: Transcription, open reading frames
Feb 03  
4 Feb 08   Graphics, Objects
Zelle chapter 5 (skip 5.5-5.6)
Notes on the Graphics Library
Lab4: Genotype to Phenotype mapping
Feb 10 Quiz 2
Quiz 2 Study Guide
5 Feb 15   Functions, Objects
Zelle chapter 6
Lab5: Evolving Faces
Feb 17  
6 Feb 22   while Loops, More Functions
Zelle chapter 8
Lab6: Population genetics
Feb 24 Quiz 3
Quiz 3 Study Guide
7 Mar 01   Top Down Design, File I/O
Zelle chapter 9, section 4.6
Mar 03  

Mar 08

Spring Break

Mar 10

8 Mar 15   Searching, Analysis of Algorithms
Zelle section 13.1
Lab7: Protein alignment
Mar 17 Quiz 4
Quiz 4 Study Guide
9 Mar 22   Sorting, Analysis of Algorithms
Zelle sections 13.2-13.3
Mar 24 Last day to declare CR/NC or W (Mar 25)
10 Mar 29   Recursion
Zelle sections 13.1-13.3
Lab8: Creating fractal images
Mar 31  
11 Apr 05   Defining new classes
Zelle chapter 10
Lab9: Simulating diffusion
Apr 07 Quiz 5
Quiz 5 Study Guide
12 Apr 12   Object Oriented Design
Zelle chapter 12
Lab10: 2D Modeling
Apr 14  
13 Apr 19   Linked lists
Lab11: Game of Life
Apr 21 Quiz 6
Quiz 6 Study Guide
14 Apr 26   Advanced Topics, Wrap-up
Apr 28  

May 07

Final Exam 2-5pm Sci 101