V. Kumar (Room: 550J) and D. Dinakarpandian (Room: 550E)

Student level:       Junior/Senior (Undergraduates) or Graduates.

Place:                  FH262.      Date and Time: MW and 3:30 PM to 4:45 PM.

Textbooks and reading material

Lecture notes and Bioinformatics Computer Skills by Cynthia Gibas and Per Jambeck.  O’Reilly

Objectives

The objective of this introductory course is to develop a clear understanding of the discipline of Bioinformatics and to prepare students to handle both fundamental and applied work in pharmaceutical companies.

It will present the complementary aspects of data management and modeling in Biological sciences.  It will cover essential basic topics in data structures and algorithms with a focus on Biological sciences to show how Computer science is complementary and useful in dealing with Biological information processing requirements.  Therefore, the course contents will be based on the selective integration of a set of topics from Biological sciences and database management.  This course will also prepare students for conducting research in the area of biological databases.

Prerequisite for undergraduate students: Exposure to computer programming and a basic background in math and science is required. Other students wishing to enroll will require permission from the instructor.

Prerequisite for graduate credit: CS352 (Introduction to Data Structures).

Course Description

It shall cover the following topics from biological and information management sciences that are central to Bioinformatics.

Topics

1.     Genetic, Molecular and Probabilistic basis of biological research.

2.     Sequence and Structural analysis of Biopolymers.

3.     Introduction to Data structures and File organizations.

4.     Information modeling and Visualization.

5.     Relational data model and Data processing.

6.     Biological databases.

7.     Query processing.

8.     Basic programming in SQL and Perl.

9.     Introduction to Data mining.

10.  Introduction to Bioinformatic software.

11.  Introduction to system-wide studies using Proteomic and Genomic approaches.

12.  Introduction to Pharmacogenomics.

 

Undergraduates

No special requirements for undergraduate students other than homework and tests.

Graduate credit

For graduate credit a students must satisfy the following requirements:

          i.     Submission of a critique of assigned journal papers on a specific topic.

          ii.     Assignment of supplemental reading material to gain in-depth knowledge of algorithms central to Bioinformatics.

          iii.     Completion of a Bioinformatics project.

          iv.     Homework and exams may be more challenging in nature.

Homework

Total homework point: 20.  Total number of homeworks will be 3 or 4. Each homework will be graded out of 20 points and at the end the final homework score will be computed as (HW1 score + HW2 score +  …  + HWn score) ÷ n.

Project

Total project point: 16.  There will either a group or individual project.  A group size will not be more than 2 students.

Tests

There will be three tests.  Test1:  16 points.   Test 2:  20 points.   Final:  28 points.

Grading Range

A   = 95 – 100       B+  = 84 - 89.         C = 55 - 64.           D = 45 - 54.

A-  = 90 – 94         B    = 70 – 83

                              B-   = 65 – 69

Note: These ranges are nearly fixed. However, depending upon students' performance, they may change slightly. The project will be either an extension of homework or could be different.

Tentative Test Dates

The following are tentative test dates. The dates of test 1 and test 2 will be finalized after consulting with students.  Test1 and Test 2 will be conducted during the class time, i.e., 3:30 PM to 4:45 PM.

Test 1: Wed., Sept. 25, 02.  Test 2: Wed., Oct. 30, 02.  Final: Tue., Dec. 17, 02 (1:00 to 3:00 PM)

 

Important points to remember

1.     You are expected to know and observe the particulars of this handout.  I follow them rigorously. Ignorance of their contents WON'T excuse you from the consequences of not following the directives they contain.

 

2.     It is important that every student must work on the homework and projects individually unless stated otherwise, and they must turn them in on time. Failure to submit two or more homework and/OR Project will earn an "F" irrespective of your performance in tests.  If, however, there is a substantiated sufficient reason (the obstacle must be something out of the ordinary and beyond your reasonable control such as serious illness or something comparable, extended computer breakdown, etc.) for the tardiness, there will be no penalty provided the homework is turned in at a time agreed upon by you and me. YOU MUST INITIATE any discussion in this direction. Hearing nothing I will presume that there is no sufficient excuse and act accordingly. Two or more identical programs will not be accepted and involved students will receive an F (irrespective of their grades in other homework and tests) as their final grade. It is to be remembered that identical programs means coding identical algorithms where variable names may or may not be the same.

 

3.     Every student must come on time. No latecomer will be allowed after the classroom door is closed. If you have a valid reason for coming late in the class, then I must have your request in writing stating the reason for not be able to come on time.

 

4.     I will not provide any programming help. However, I will be happy to discuss any programming problem.

 

5.     It is students' responsibility to find out what was covered in the class during his/her absence. Such absence from the class will not be accepted as a reason for not submitting the homework on time or for obtaining a poor score in tests.

 

6.     There is no academic assessment for withdrawal before or on October 22, 2002. After this date an academic assessment of "W" or "WF" will be made.

 

7.     Incomplete (I) grades will not be given for failing to complete the course work on time or obtaining poor scores in tests or homework.

 

8.     Change from Credit to Audit: The instructor is the only person that may authorize change in status from regular to audit. The last date for this change is September 24, 2002.  The student must have a grade of "C" or better.  No requests to change to audit will be granted after this date.

 

9.     All tests will be closed books and notes.

 

10.  University regulations do not permit to post your grades anywhere.  Also I am not allowed to leave your graded homework, tests, or project to an unattended place.  These materials will be deposited to Student Services office and you will be required to collect them from there.

Enjoy the course