CS21B:Intro to Computer Science with Applications in Biology
Spring 2012

Class Info | Schedule | Lab Sessions | Study Sessions | Tips for Success |
| Grading | Code Style | Academic Integrity | Academic Accommodations | Links


  • There will be two review sessions for the final exam. Tuesday, May 1 from 1-4pm with Rich and Ameet and Wednesday, 7-9pm with the ninjas. Both sessions will be in Science Center 240.
  • The Final Exam study guide has been posted below. As a reminder, the final exam is May 3 from 7-10pm in Science Center 101

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This syllabus is a living document; please be aware that many elements on this page will change throughout the semester, including the course schedule. It is the student's responsibility to review this page periodically for updates.

Class Info

Section 1: Tuesday, Thursday 9:55–11:10am, Science Center 240
Professor: Ameet Soni
Office: Science Center, Rm 253 Office hours: 10:00-noon Monday, or by appointment

Welcome to CS21B. This course will introduce fundamental ideas in computer science while also teaching you how to write computer programs while exposing you to 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 will be 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 the usual first course 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 CS 33 or CS 35.

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: Frances Ruiz (office: 257 Sci Ctr phone: x6062)
CS21 Ninjas (student mentors): Sarah Chasins and Leah Foster will be specifically assigned to our class (CS21B) and will be most able to help you with the lab assignments as well as with in-class problems. Other ninjas, helping all sections of CS21, include: Mark Serrano, Brandon Snuggs, Samantha Goldstein, and Sophie Libkind. These students can help you with general programming concepts and assist you in studying for quizzes.

Study sessions

The CS Ninjas will assist me in class and run study sessions in the main CS lab (Science Center 240) on the following evenings:

Day Time Location
Sundays 7-10pm Sci Center 240
Wednesdays 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 lab 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 Sessions

CS21B will have a lab session every Monday from 2:40-4:10pm in Science Center 240. The CS lab is open 24 hours a day, 7 days a week for you to use for CS21 lab assignments. These lab sessions are designed to provide additional hands-on programming to understand lecture concepts as well as for assistance with weekly lab assignments.

Accessing the CS labs after hours

You can use your ID to gain access to the computer labs 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. For this class, your ID will give you access to the labs in rooms 238 and 240.

How to Succeed in this class

Academic Accommodations

If you believe that you need accommodations for a disability, please contact Leslie Hempling in the Office of Student Disability Services, located in Parrish 130, or e-mail lhempli1 to set up an appointment to discuss your needs and the process for requesting accommodations. Leslie Hempling is responsible for reviewing and approving disability-related accommodation requests and, as appropriate, she will issue students with documented disabilities an Accommodation Authorization Letter. Since accommodations may require early planning and are not retroactive, please contact her as soon as possible. For details about the Student Disabilities Service and the accomodations process, visit the Office of Student Disability Services.

You are also welcome to contact me privately to discuss your academic needs. However, all disability-related accommodations must be arranged through Leslie Hempling in the Office Of Student Disability Services.

To receive an accommodation for a course activity, you must have an Accomodation Authorization letter from Leslie Hempling and you need to meet with me to work out the details of your accommodation at least one week prior to the activity.


Grades will be weighted as follows:
40%Lab assignments
25%Final Exam
05%Class Participation

Quiz policy

Quizzes will be given at the beginning of class on the days posted in the Announcements section of the Schedule. Please look over these dates carefully and contact the professor in advance if you cannot be in class for a quiz.

If you are not present at the start of class on the day of a quiz, but make it to class before the end, then you may take the quiz. Otherwise you will receive a zero for that quiz.

Lab assignment policy

Programming assignments will typically be assigned Wednesday or Thursday of each week and will be due 11:59 pm, Tuesday the following week. You are strongly encouraged to start early and to attend the study sessions for extra practice.

You will submit you assignments electronically using the handin21 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 at least a day before the deadline with a legitimate reason for needing extra time, such as an illness.

Even if you do not fully complete an assignment, you should submit what you have done to receive partial credit. Unless otherwise stated, labs are to be completed individually. Please carefully read the statement on academic integrity for more information.

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:

  • A comment at the top of the program that includes
    • Program authors
    • Date or Dates
    • A brief description of what the program does
  • Concise comments that summarize major sections of your code
  • Meaningful variable and function names
  • Function comments that include: (1) description of what function does; (2) description of input values (parameter values); (3) description of return value(s)
  • Well organized code
  • White space or comments to improve legibility
  • Avoidance of large blocks of copy-pasted code
Also, look over the Python Code Style Guide for more details and some examples of good code style.

Academic Integrity

Academic honesty is required in all work you submit to be graded. 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.


This is a tentative schedule; it may change as we go.
1 Jan 17 Using Unix (240 SciCntr):
Tue., 4-5pm
Wed., 8-9pm
Introduction to Python and Unix
Zelle Chapt. 1-2
Useful Unix commands
Getting started with python and Unix
In class: Thursday
Assn: Lab 0: Unix and vim
Assn: Lab 1: Simple Programs
Jan 19  
2 Jan 24 Quiz 1 Study Guide Numbers and Strings
Chapt. 3, 4.1, 4.2
In class: Tuesday, Thursday
Assn: Lab 2: Population Growth
and Translation
Jan 26 Quiz 1
add/drop ends (Jan 27)
3 Jan 31   if/else Booleans
Chapt. 7.1, 7.2, 7.3 and 8.4.1, 8.4.2
In class: Tuesday, Thursday
Assn: Lab 3: Transcription
Feb 02  
4 Feb 07 Quiz 2 Study Guide Graphics, objects
Chapt. 5 (skip 5.5, 5.6)
notes on the Graphics Library
In class: Tuesday, Thursday
Assn: Lab 4: Fun with Graphics
Feb 09 Quiz 2
5 Feb 14   Functions, Objects
Chapt. 6 (skip 6.3)
In class: Tuesday, Thursday
Assn: Lab 5: Snail Race
Assn: Worksheet
Feb 16  
6 Feb 21 Quiz 3 Study Guide while Loops, More Functions
Notes on strings and lists as objects
Notes on using the random library
Chapt. 8.1, 8.2, 8.3, 4.4
In class: Tuesday, Thursday
Assn: Lab 6: Hardy Weinberg
Feb 23 Quiz 3
7 Feb 28   Top Down Design, File I/O
Chapt. 9.1, 9.2, 9.3, 4.6
In class: Tuesday
Mar 01  

Mar 06

Spring Break

Mar 08

8 Mar 13   More Top Down Design, File I/O
Chapt. 9.1, 9.2, 9.3, 4.6
notes on File I/O
In class: Tuesday
In class: Thursday
Assn: Lab 7: Protein Alignment
(Top Down Design)
Mar 15  
9 Mar 20 Quiz 4 Study Guide Searching, Analysis of Algorithms
Chapt. 13.1
In class: Tuesday, Thursday
Assn: Lab 7: Protein Alignment
Mar 22 Quiz 4
10 Mar 27   Sorting, Analysis of Algorithms
Ch. 13.2-13.3
In class: Tuesday, Thursday
Assn: Lab 8: Zipcodes
Search & Sort worksheet
Mar 29  
11 Apr 03 Quiz 5 Study Guide Recursion
Chapt. 13.1-13.3
In class: Tuesday, Thursday
Assn: Lab 9: Global Alignment
Apr 05 Quiz 5
12 Apr 10   Defining New Classes
Chapt. 10.1, 10.3, 10.4
In class: Tuesday, Thursday
Assn: Lab 10: The Swindle
Apr 12  
13 Apr 17 Quiz 6 Study Guide Linked lists
In class:
Assn: Lab 11: Bacteria Colony
Apr 19 Quiz 6
14 Apr 24   Wrap-up
Apr 26 Final Exam Study Guide

May 03

Final 7:00pm–10:00pm Sci 101

Links that are related to the course may be posted here. If you have suggestions for links, let me know.