CSCI 329: Introduction to Bioinformatics - Fall 2013

Course Information

Lectures:

MWF 11:00 - 11:50 AM
Place: KH 238 Computer Science Lab - Back Room

Professor:

Yana Kortsarts, Computer Science
Office:
Phone: (610) - 499 - 4367
e-mail: ykortsarts@mail.widener.edu
homepage: http://cs.widener.edu/~yanako

Office Hours:

• Yana Kortsarts
  Place: Kirkbride 266 A
  Time:

  • Monday: 12:00 - 1:00 PM
  • Tuesday: By appointment
  • Wednesday: 12:00 - 1:00 PM, 3:50 - 4:20 PM
  • Thursday: 12:00 - 1:00
  • Friday: 9:20 - 9:50 AM, 1:00 - 3:00 PM
  • Monday and Wednesday: 9:20 - 9:50 - By appointment

  To make an appointment, please, send an e-mail ykortsarts@mail.widener.edu

References

• Bioinformatics, A practical Guide to the Analysis of Genes and Proteins, Andreas D. Baxevanis, B.F. Francis Ouellette, John Wiley & Sons, Inc, ISBN 0-47138390-2
• Fundamental Concepts of Bioinformatics, Dan E. Krane, Michael L. Raymer, Pearson Education, ISBN 0-8053-4633-3
• Evolutionary Computation in Bioinformatics, Gary B. Fogel, david W. Corne, Morgan Kaufmann Publishers, ISBN 1 - 55860-797-8
• An Introduction to Bioinformatics Algorithms, Neil C. Jones, Pavel A. Pevzner, The MIT Press
• Developing Bioinformatics Computer Skills, Cyntia Gibas and Per Jambeck
• Ethics, Computing, and Genomics Herman Tavani, Rivier College, Jones and Bartlett Publishers
• Biopython tutorial and information on http://www.biopython.org

Course Description

Bioinformatics is a new field that integrates Computer Science, Biology, and Information Technology to manage, analyze, and understand biological, biochemical and biophysical information. According to the National Institute of Health (NIH) definition, bioinformatics is “research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, analyze, or visualize such data.” This course is an interdisciplinary course that will be taught by the team from Computer Science and Biology departments. The course introduces the basic computational concepts and methods used in molecular biology and molecular genetics, introduces students to the analysis of genetic sequences. The course discusses available computational tools for extracting biological information from DNA and protein sequences. The course provides a brief introduction to bioinformatics algorithms. In this course you will work with PYTHON in UNIX environment.

Tentative Course Topics:

• Advanced Python - One-Dimensional and Two-Dimensional Lists, Tuples, Dictionaries, Regular Expressions, File I/O
• Introduction to Molecular Biology
• Sequence Alignment
• Bioinformatics Algorithms: Global and Local Alignment Dynamic Programming Algorithms
• BLAST
• Working with Sequence Databases: NCBI
• Ethical and Societal Issues

Course Goals and Objectives

This course will provide an introduction to bioinformatics to interpret the rapidly expanding amount of biological information. Course will discuss the basic concepts of bioinformatics and introduce students to the introductory algorithms and computational tools to conduct DNA & Protein sequence analysis. After completion of this course students will be able to design computational implementations for introductory bioinformatics algorithms, apply computational tools to analyze DNA & Protein sequences, understand societal and ethical issues related to bioinformatics.

Useful Links

• The National Center for Biotechnology Information (NCBI): http://www.ncbi.nlm.nih.gov
• The DNA Learning Center
• Molecules of Genetics
• The Institute of Genomic Research - TIGR
• Biology Workbench
• DNA Interactive
• European Molecular Biology Laboratory
• DNA Data Bank of Japan
• BEDROCK (Bioinformatics Education Dissemination: Reaching Out, Connecting, and Knitting-together)
• Biopython tutorial and information on http://www.biopython.org

Policies

Attendance Policy

The University's policy will be applied. Students who miss class are always responsible for obtaining class assignments. All assignments and class materials are available through this website.

In this course ATTENDANCE IS REQUIRED. Class Participation and Attendance is 10% of the final grade.

Academic Fraud

The Science Division strictly enforces the University's policy on cheating and other forms of academic fraud.

Student Academic Grievance Procedure

If a student has a grievance concerning a class in which he/she is enrolled, he/she will first try to resolve the problem with the instructor of the class. If it is impossible to resolve the matter at this level, then the grievance must be placed in writing and appealed in the following order:
• Division or Program Head
• Dean of Arts and Sciences (Arts and Sciences Academic Council)
• Provost of the University
• University Academic Council
All student grievances will first be referred to the class instructor before they are treated at the level of the Division Head.
For Standards for Academic Integrity, Appeal Procedures for Student Academic Grievances, and Attendance Policy please see Student Handbook and Widener's Undergraduate Catalog:

Student Handbook
Widener's Undergraduate Catalog

Electronic Devices in the Classroom

• NO CELL PHONES. Cell phones must be turned off for the duration of the lecture and lab.
• All electronic devices except cell phones are permitted

Evaluation Criteria (Grading)

There will be:

• reading and home assignments
• 1 reading and presenting research paper assignment
• 1 in-class final project and final presentation of the results
• In-class laboratory assignments and mini - quizzes

The work handed in must be the student's own work. Assignments which are written in groups are easily identifies and
will receive grades of 0 for all participants.

Final Grade

Reading and Home Assignments	5%
Reading and Presenting Research Paper Assignment	15%
In-class Laboratory Assignments	35%
Attendance	10%
Final Project and Presentation	35%
Total	100%

Final Grade Table

A:	95 - 100
A-:	90 - 94
B+:	87 - 89
B:	83 - 86
B-:	80 - 82
C+:	77 - 79
C:	73 - 76
C-:	70 - 72
D+:	67 - 69
D:	60 - 66
F:	59 - 0