BIOL200 2013

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BIOL 200 Cell Biology II LAB, Spring 2013

Hunter College of the City University of New York

Course information

Instructors: TBD

Class Hours: Room TBD HN; TBD

Office Hours: Room 830 HN; Thursdays 2-4pm or by appointment

Contact information:

  • Dr. Weigang Qiu:, 1-212-772-5296

Experiment #4

The Tree of Life and Molecular Identification of Microorganisms


To classify microorganisms and determine their relatedness using molecular sequences.


CELL BIO II Experiment #4:

  • Introduction1 point:
Statement of objectives or aims of the experiment in the student’s own words.(not to be copied from the Lab Manual)
  • Evaluate and interpret computational results statistically ("Statistical-thinking")
  • Formulate informatics questions quantitatively and precisely ("Abstraction")
  • Design efficient procedures to solve problems ("Algorithm-thinking")
  • Manipulate high-volume textual data using UNIX tools, Perl/BioPerl, R, and Relational Database ("Data Visualization")


This 3-credit course is designed for upper-level undergraduates and graduate students. Prior experiences in the UNIX Operating System and at least one programming language are required. Hunter pre-requisites are CSCI132 (Practical Unix and Perl Programming) and BIOL300 (Biochemistry) or BIOL302 (Molecular Genetics), or permission by the instructor.


Krane & Raymer (2003). Fundamental Concepts of Bioinformatics. Pearson Education, Inc. (ISBN 0-8053-4633-3)

This book should be available in the Hunter Bookstore, as well as through several popular retailers and resellers online.

Grading & Academic Honesty

Hunter College regards acts of academic dishonesty (e.g., plagiarism, cheating on examinations, obtaining unfair advantage, and falsification of records and official documents) as serious offenses against the values of intellectual honesty. The College is committed to enforcing the CUNY Policy on Academic Integrity and will pursue cases of academic dishonesty according to the Hunter College Academic Integrity Procedures.

Student performance will be evaluated by weekly assignments and projects. While these are take-home projects and students are allowed to work in groups and answers to some of the questions are provided in the back of the textbook, students are expected to compose the final short answers, computer commands, and code independently. There are virtually an unlimited number of ways to solve a computational problem, as are ways and personal styles to implement an algorithm. Writings and blocks of codes that are virtually exact copies between individual students will be investigated as possible cases of plagiarism (e.g., copies from the Internet, text book, or each other). In such a case, the instructor will hold closed-door exams for involved individuals. Zero credits will be given to ALL involved individuals if the instructor considers there is enough evidence for plagiarism. To avoid being investigated for plagiarism, Do Not Copy from Others & Do Not Let Others Copy Your Work.

Submit assignments in Printed Hard Copies. Email attachments will NOT be accepted. Each assignment will be graded based on timeliness (10%), completeness (30%), whether executable or having major errors (20%), correctness of the final output (20%), algorithm efficiency (10%), and cleanness and readability in programming styles (10%).

The grading scheme for the course, is as follows (Subject to some change. You will be notified with sufficient time):

  • Assignments (50%): 10 exercises.
  • Mid-term (20%): In class Assignment + Take home to be collected on the same day.
  • Final exam (20%)
  • Classroom Q & A (5%): Read the chapters before lecture.
  • Attendance (5%): 1-2 absences = -2.5%. More than 2 = -5%.

Programming Assignment Expectations

All code must begin with the lines in the Perl slides, without exception. For each assignment, unless otherwise stated, I would like the full text of the source code. Since you cannot print using the text editor in the lab (even if you are connected from home), you must copy and paste the code into a word processor or a local text editor. If you are using a word processor, change the font to a fixed-width/monospace font. On Windows, this is usually Courier.

Code indentation is your personal taste, so long as it is consistent and readable. Use comments whenever you think either the code is unclear, or simply as a guideline for yourself. Well-commented code improves readability, but be careful not overdo it.

Also, unless otherwise stated, both the input and the output of the program must be submitted as well. This should also be in fixed-width font, and you should label it in such a way so that I know it is the program's input/output. This is so that I know that you've run the program, what data you have used, and what the program produced.

If you are working from the lab, one option is to email the code to yourself, change the font, and then print it somewhere else as there is no printer in the lab.

Course Schedule (All Saturdays)

Dates and assignments below are subject to some change

"Lecture slides" links will be available either during or before each lecture, in PDF.

Homework assignments are due the week *after* the date under which they appear. ie, an assignment posted under Jan 29 is due the following lecture, on Feb 5.

January 29

  • Course Overview
  • Tutorial: UNIX Account, Tools, & Emacs [Lecture Slides]
  • UNIX Tutorial: Please check the new #Useful Links section below
  • How to connect remotely: (Windows) (Mac)
  • Homework: This homework will *not* be graded. It is for practice purposes ONLY.

February 5

February 12


(Read Chapter 6 for next class)

February 19

Yozen will not be lecturing

  • Chapter 6. Gene and Genome Structures [Lecture Slides Lecture Slides Ch.6-Che
  • Tutorial: ORF Prediction using GLIMMER
  • Homework: This homework will be graded.

February 26

March 5

March 12

March 19


March 26


April 2

April 9

April 16

  • Topic: Relational Database and SQL
  • Tutorial: the Borrelia Genome Database
  • Homework: SQL-embedded PERL

April 23

NO CLASSES (Spring recess)

April 30

May 7

  • Chapter 6 (Gene Expression) & Chapter 8 (Proteomics)
  • Tutorial: Array Data Visualization and Analysis ( Micro-Array Analysis Slides)
  • Homework:Data Analysis using R

May 14

  • Chapter 7. Protein Structure Prediction

May 21

  • Final Project Due (TBA)

Useful Links

Unix Tutorials

Perl Help

  • Professor Stewart Weiss has taught CSCI132, a UNIX and Perl class. His slides go into much greater detail and are an invaluable resource. They can be found on his course page here.
  • Perl documentation at Besides that, running the perldoc command before either a function (with the -f option ie, perldoc -f substr) or a perl module (ie, perldoc Bio::Seq) can get you similar results without having to leave the terminal.



R Project

  • Install location and instructions for Windows
  • Install location and instructions for Mac OS X
  • For users of Ubuntu/Debian:
sudo apt-get install r-base-core
  • For users of Fedora/Red Hat:
su -
yum install R


Other Resources

© Weigang Qiu, Hunter College, Last Update Jan 2013