Course Syllabus and
Overview -- Bioinformatics
CSC 385/685; PHY 327/627; BICM 715
Instructors: Drs. David John
and Jacquelyn Fetrow
Office: John: West 251;
Fetrow: West 236 & Olin 301B
Email: djj@wfu.edu,
fetrowjs@wfu.edu
Office Hours: TBA
Course meeting time: T,
Th 1:30pm, West 017.
This course will be taught using the
"Studio Style" of instruction. Generally there will be a 45
minute lecture followed by an inclass 45 minute related
laboratory. For the laboratory portion the students will work in
teams with both computer scientists and biologists as members.
Course requirements:
CSC 385/685: To get credit for this course
number, students will
be required to actively participate in the software engineering and
algorithm design aspects of the course. All students will be
required
to understand the research issues and master the key concepts in the
field of bioinformatics.
BICM 715; PHY 327/627: To get credit for
this course number,
students will be required to master the biotechnical details behind the
projects and effectively communicate those details to the students who
are doing the engineering and algorithm design. All students will
be
required to understand the research issues and master the key concepts
in the field of bioinformatics.
Course numbers and prerequisites:
CSC 385/685: Prerequisite for
registering for this course number is CSC 221 (or permission of the
instructor).
BICM 715; PHY 327/627: Prerequisites
for registering for this
course number are introductory courses in biology, chemistry, and
molecular biology or biochemistry (or permission of the instructor).
Textbooks:
Neil Jones & Pavel
Pevzner (CS students)
Bioinformatics Algorithms
MIT Press
isbn 0 262 10106 8
Dan Krane & Michael Raymer (Biology students)
Fundamental Concepts of BioInformatics
Benjamin Cummings
isbn 0 8053 4633 3
It is not possible to cover all topics
in these textbooks during
a single semester. You will not be responsible for knowing those
chapters that we do not cover in class, laboratory, or during the
project. We strongly advise each of you getting a book
buddy with whom you can share the "other" book.
Other References(s):
Jacque Cohen, "Bioinfomatics--an introduction for
computer scientists", ACM Computing
Surveys, Volume 36, Issue 2, June 2005, pages 122-158.
Access through ACM Portal .
Roger Pressman. Software Engineering: A Beginner's
Guide. McGraw Hill. 1988. Available from D.
John.
Reading assignments
and quizzes:
Reading and review assignments (see schedule
below) are to be done prior to class. Online reading quizzes, due
before every lecture, cover the material in the current and previous
reading assignments.
These will be due by 10 am the day of class. The
reading quizzes are to be completed without any assistance.
Points can
not be earned on these assignments when there is an associated
unexcused absence form class on the same day.
Research-based learning: The
best way to learn to use bioinformatics
and computational biology methods is to apply those methods in a
research-based format. We will follow this learning approach in this
course. We will teach methods and theory, but you will apply the
methods and theory to a problem for which we do not yet know the “right
answer;” however, it is a problem in which we are interested. The
project topic will be presented in more detail in several weeks.
Grading:
Reading quizzes (18 quizzes at 4
points each) 72 points
Laboratory exercises (8 at 50 points
each) 400 points
Project parts
340 points
(scope v1, 50 points; scope v2, 50;
scope presentation, 20; design v1, 50;
design v2, 50; design presentation, 20;
documentation, 50; user training session, 50)
Final project
100 points
Class participation,
attendance,
50 points
observations, and creativity
Midterm examination
200
points
Final examination
200 points
Total: 1262 points
Graduate credit: Students
registered for any of the graduate course
numbers and receiving graduate credit will be held to higher
expectations than students receiving undergraduate credit. Graduate
students will be expected to answer lab and exam questions in more
detail. Often, there will be an additional, more difficult
question
that graduate students must answer in addition to the other questions,
so the total number of allowed points will be higher for graduate
students. Graduate students are expected to participate in class
more
often and to offer more insightful observations.
Software/hardware required: A
laptop computer is required for this
class. You must bring the laptop computer to each class,
as we will usually be connecting to the internet to learn to use
bioinformatics tools. Students registered for one of the CSC
course
number will be required to utilize certain programming tools and
languages.
Tentative Schedule
August 24 -- Introductions to Algorithms and BioChemistry
Reading Assignment-- K&R:
1:2-14 & 1:19-26
J&P: 1 & 3:57-67, 75-78
----------------------------------------------------
*August 30 -- Central Dogma
*September 1 -- Introduction to the project
Reading Assignment -- the tutorial found at
http://courses.cs.vt.edu/csonline/SE/Lessons/Waterfall
*September 6 -- Project Requirements (1)
*September 8 -- Pairwise Sequence Alignment
Reading Assignment -- K&R: 2
J&P: 6.1-6.9, 9:324-331
*September 13 -- Pairwise Sequence Alignment
*September 15 -- Project Requirements (2)
Scope Version 1 Document Due
----------------------------------------------
*September20 -- Group meetings about Scope Documents
*September 22 -- Pairwise Sequence Alignment
*September 27 -- Pairwise Sequence Alignment
September 29 -- Scope Presentations by groups
Scope Version 2 Document Due
---------------------------------------------
*October 4 -- Project Review and Design Document
October 6 -- MIDTERM EXAM
October 11 -- Gene Prediction and regulatory regions
K&R: 6 (pages 117-142)
J&P: 4.4-4.6, 67.11-6.13, 11
October 13 -- Gene Prediction and regulatory regions
-----------------------------------------
*October 18 -- Protein Secondary Structure
Reading Assignment -- K&R: 7
J&P: TBA
*October 20 -- Protein Secondary Structure
Design Version 1 Document Due
*October 25 -- Protein Secondary Structure
*October 27 -- Protein Secondary Structure
------------------------------------------
November 1 -- Project Review
November 3 -- Design Presentations by groups
Design Version 2 Document Due
------------------------------------------
*November 8 -- Phylogenetic Trees
Reading Assignment -- K&R: 4-5
J&P: 10
*November 10 -- Phylogenetic Trees
*November 15 -- Phylogenetic Trees
*November 17 -- Phylogenetic Trees
-------------------------------------
November 22 -- Project Review
November 29 -- User Training
December 1 -- User Training
December 8 -- FINAL EXAM (PM)
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Last modified: Wed, 28 Sep 2005 16:30:30 GMT