Intro to Bioinformatics
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Instructor:
Dr. Zhong
Zhong--Hui Duan
Office: 238 CAS
Office Hours:
MF12:00--1:00, TTh6:00
MF12:00
TTh6:00--6:30, other times by appointment
Prerequisite:
3460:210 Computer Science II
Objectives:
 provide students with a broad scope of the field of
bioinformatics; to communicate the fundamental methods
and techniques in bioinformatics; and to discuss major
topics and statestate-of
of--art research in bioinformatics.
Topics
Part 1:
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Part 2:
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Mitchell L. Model, Bioinformatics Programming Using Python:
Practical Programming for Biological Data, O'Reilly Media; 1st
edition (December 22, 2009). Safari online:
http://proquest.safaribooksonline.com.proxy.ohiolink.edu:9099
/book/programming/python/9780596804725..
/book/programming/python/9780596804725
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Overview of protein structures and terminology
RNA secondary structure prediction
Part 4
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Microarray, next generation sequencing, and gene ontology
Expression data analysis
Recommended Texts
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Neil C. Jones and Pavel A. Pevzner,
Pevzner, An Introduction to
Bioinformatics Algorithms, MIT Press, 2004.
Mitchell L. Model,
Bioinformatics
Programming Using
Python: Practical
Programming for
Biological Data,
O'Reilly Media, 2009
Dan E. Krane and Michael L. Raymer,
Raymer, Fundamental Concepts of
Bioinformatics,, 2003, Benjamin Cummings, ISBN: 0Bioinformatics
0-80538053-46334633-3.
Materials supplied by the Instructor
Recommended Texts
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Sequence alignment and searching
Phylogeny construction
Part 3
Recommended Texts
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Overview of multiple genome projects and biological
databases
Intro to molecular genetics and Python
Neil C. Jones and
Pavel A. Pevzner,
An Introduction to
Bioinformatics
Algorithms, MIT
Press, 2004.
Recommended Texts
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Dan E. Krane and
Michael L. Raymer,
Raymer,
Fundamental
Concepts of
Bioinformatics,
Benjamin Cummings,
Cummings,
2003
1
Grading Policies
Software
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one midterm exam (20%),
one final exam (30%),
4 group programs (40%),
class participation, quizzes, homework (10%).
Python, Excel, Matlab,
Matlab, R and Bioconductor
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Download and Install Python
Matlab
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Bioinformatics toolbox
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Statistics toolbox
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http://www.mathworks.com/products/bioinfo/
The final is comprehensive. Late programs will be
penalized 10% per day late.
R and Bioconductor
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Grading scale (+/
(+/-- grades may be assigned at
instructor's discretion):
A 9090-100 B 8080- 89 C 70
70-- 79 D 60
60--69 F 0- 59
CS account:
http://wiki.cs.uakron.edu
activate your CS account (you have to be
on campus or use VPN)
lecture notes and other class materials
through links at your Springboard
or
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http://www.cs.uakron.edu/~zduan/class/bioinformat
ics/
Program Submissions
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Programs will be submitted using homework submission server.
server.
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You will also need to submit a printed copy of your source code.
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Change your
password to activate
your CS account
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DO NOT submit programs that are not reasonably correct! To be
considered reasonably correct, a program must be completely
documented and work correctly for sample data provided with the
assignment.
Programs failing to meet these minimum standards will be returned
ungraded and a 30% penalty assessed. Late points will be added on
top of this penalty.
Many programs will be tested against additional "hidden" data. A
minimum requirement for passing this course is the completion of all
programming assignments (each must be reasonably correct).
2
Ethics
All programming assignments must be your
own work. Duplicate or similar programs,
plagiarism, cheating, undue collaboration,
or other forms of academic dishonesty will
be reported to the Student Disciplinary
Office as a violation of the Student Honor
Code.
Dates and final exam time
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Last day to drop from this class:
class:
September 9, 2013(without WD)
October 13, 2013 (with WD)
Final Exam Time:
Time: Given according to the University
Final Exam schedule:
Friday, Dec 13, noon - 1:55pm.
Homework
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Questions?
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Download Python and make sure you can run
“hello world” program
3