Additional slides with animations to strengthen your understanding of
the central dogma of molecular biology, sickle cell anemia, etc..
Link to
biotechnology companies in the Bay Area.
Information about the Instructor
Name: Sami Khuri
Office: 418 MacQuarrie Hall
Phone: 924-5081
Office Hours:
Tuesdays and Thursdays: 10:20 to 10:45 and 13:20 to 15:00.
Catalogue Description
This practical course, cross-listed with the biology department,
provides an introduction to the main public domain tools, databases and methods
in bioinformatics, including DNA and protein databases, such as Genbank
and PDB, software tools such as
those in the Wisconsin Package, at the National Center for Biotechnology
Information (NCBI), and other web accessible applications.
More precisely, the course
introduces the methods for collecting, editing, and storing
macromolecular sequences, for pairwise and multiple sequence alignments,
for database searching for similar sequences, and for phylogenetic
prediction.
This course is intended both for biology and
computer science
students, to work together to solve complex biological questions requiring
the use of standard bioinformatics applications and databases.
Textbook
Textbook Reading
Guidelines Last update: November 1, 2008.
Biology Terms
Understanding Bioinformatics
by Marketa Zvelebil and Jeremy Baum,
Garland Science, 2008, ISBN 0-815-34024-9.
The book can be found at the bookstore under CS123A.
- We shall cover most of the topics from chapters 1, 2, 3, 4 and 7.
- Before reaching the end of a chapter, I will announce which topics
of the following chapter will be covered cover.
- Please bring the book to every class meeting.
- A copy of my powerpoint slides (6 per page) will be available
to the students enrolled in the class.
Course Objectives
To promote cross-disciplinary communication between the two fields:
Biology and Computer Science.
Use case studies in homework and in-class hands-on exercises to extract
generalizable concepts.
To acquaint students with some of the most challenging
problems in life science and show how computer science can be used to
solve some of these problems.
Phylogenetic tree construction
Upon successful completion of this course, students should be able to
use dynamic programming for pairwise alignment, to understand how
multiple sequence alginment algorithms work, to have a clear understanding
of Fitch-Margoliash, UPGMA and neighbour-joining phylogenetic tree
algorithms, and to know various databases for DNA and protein sequences.
Course Requirements
- Dual Role of DH450: Lecture/Lab
DH450 is a dual purpose room. It can be a regular
lecture room or it can be a computer laboratory. Please
note that OR in the last sentence is exclusive. In other
words, DH450 is never a lecture room AND a computer lab
at the same time.
Lecture Mode: This is when DH450 is used as a regular lecture room.
Students are expected to listen and follow the lecture. DH450 is a noisy
room because of the large number of workstations and the server.
Be considerate to your classmates and follow the lecture.
Do not use the computer (workstation) and do not talk to your
classmates. Do not open your laptops. If you are addicted
to checking mail, chatting, surfing the internet, etc...,
and cannot follow these simple rules, please do not enroll
in this class.
Lab Mode: This is when DH450 is used as a computer lab. Use the
computers and share your ideas and solutions with your classmates.
We shall alternate between the two modes.
A typical class will begin with a short lecture (Lecture Mode)
followed by a hands-on (Lab Mode).
We will have a number of hands-on exercises.
The purpose of the hands-on exercises is to develop your
understanding of the material.
Tentative Schedule:
August 26 to September 9: Introduction to Molecular Biology and to
Bioinformatics
September 9 to October 2: Pairwise Sequence Alignment
October 7 to October 28: Multiple Sequence Alignment
November 4 to December 2: Phylogenetic Inference
- Problem Sets:
Five homework assignments.
The purpose of the assignments is to develop your understanding
of the material and your skills in problem-solving.
Only a subset of the assigned problems on any given problem set
will be graded.
No late homework will be accepted. However,
under exceptional circumstances, one problem set
per student might be accepted late.
It will need to be handed in prior to the following class meeting and
will be graded with 30% off. Such an extension should be requested
from the instructor.
Any homework not picked up during
class time will be left on the shelves near my
office door.
Assignments are due in the beginning of the lecture
on the following dates:
- HW One in pdf and in
MS Word
due on Thursday, September 11, 2008.
Please note that you need the book to be able to solve Problem 1.
The book can be found at the bookstore under CS123A.
- HW Two in pdf and in
MS Word
due on Thursday, September 25, 2008.
- HW Three in pdf and in
MS Word
due on Thursday, October 16, 2008.
- HW Four in pdf and in
MS Word
due on Thursday, November 6, 2008.
The eight sequences
myh16_sequences.txt needed for Problem Five.
- HW Five in pdf and in
MS Word
due on Thursday, November 20, 2008.
The article
Multiple founder effects and geographical clustering
of BRCA1 and BRCA2 families in Finland needed for
Problem Two, Part a.
The article
Novel Germline BRCA1 and BRCA2 Mutations in
Breast and Breast/Ovarian Cancer Families from the
Czech Republic needed for
Problem Two, Part b.
Cover sheet for all assignments
- Term Project:
Information about the project can be
found here. The
Team Formation is
due on Tuesday, October 14, 2008. The Progress Report is due on
Thursday, November 13, 2008 at the begining of the class. The final
project is
due on Thursday, December 4, 2008 at the beginning of the lecture.
The article for Project One.
The article for Project Two.
The book for Project Three and Project Four can be found on reserve
at MLK library.
- Exams:
Exam One: Tuesday, October 7, 2008.
Exam Two: Tuesday, November 18, 2008.
Final Exam: Monday, December 15, 2008, from 7:15 to 9:30am.
Exam One and Exam Two are each one hour and fifteen minutes
long. All exams are in-class,
closed-book and comprehensive. You will get back your exams
within one week at which time we'll go over them in class.
Exams will be collected and kept with me.
Make-up exams will be given only at the instructor's discretion.
Class Attendance
Class attendance is strongly encouraged.
In class, we shall cover many
topics and examples that are neither in the class notes
nor in the textbook. If you miss a lecture,
it is your responsibility to find out what was covered in
class (this includes: handouts given
out during your absence, corrected typos and errors,
examples discussed in class - that
are neither in the book nor in the notes - clarifications
and changes made to assignments or the project, etc...).
Grading Policy
The final grade will be computed as shown below:
Assignments: 20%
Exam One: 20%
Exam Two: 20%
Project: 10%
Final: 30%
[97, 100] A+
[93, 97) A
[90, 93) A-
[87, 90) B+
[82, 87) B
[80, 82) B-
[77, 80) C+
[72, 77) C
[70, 72) C-
[67, 70) D+
[62, 67) D
[60, 62) D-
[0, 60) F
Add/Drop Policy
For those wishing to add this course, the deadline is September 12, 2008.
The last day to drop with a full refund is September 5, 2008.
According to University and Department guidelines, dropping after
September 5, 2008, requires a serious and compelling
reason to drop a course.
Grades alone do not constitute reason to drop a course.
Students who stop attending without officially dropping will
be issued a U at the end of the semester which is counted as
an F in calculations of GPA. See University Catalog.
Academic Integrity
Students should read the ``Policy on Academic Integrity" in the
University Catalog. Anyone caught cheating (including copying
the work of others) on any assignment in the
class will receive a failing grade for the assignment, in addition
to other sanctions that are permitted by the University, including
but not limited to the filing of a report with the Dean
of Student Services and expulsion from the University.
Students should read the ``Policy on Academic Integrity"
in the University Catalog. The "Policy on Academic Integrity"
can be found
here.
-
Anyone caught cheating (including
copying the work of others) on any assignment in the class will
receive a failing grade for the assignment, in addition to other
sanctions that are permitted by the University, including but not
limited to the filing of a report with the Dean of Student Services
and expulsion from the University.
- Your own commitment to learning, as evidenced by your enrollment at
San
José State University, and the Universitys Academic Integrity Policy
requires you to be honest in all your academic course work. Faculty are
required to report all infractions to the Office of Judicial Affairs.
Disability Resource Center
If you need course adaptations or accommodations because of a
disability, or if you need special arrangements in case the building must
be evacuated, please make an appointment with me as soon as possible, or
see me during office hours. Presidential Directive 97-03 requires that
students with disabilities register with DRC to establish a record of
their disability.
Summer 2008 Internships and Research Programs (Most updates for
2009 will appear in mid-November)