CSCI 498:  Introduction to Bioinformatics

Description

(Exploration of selected topics in computer science.)

"Roughly, bioinformatics describes any use of computers to handle biological information. In practice the definition used by most people is narrower; bioinformatics to them is a synonym for "computational molecular biology"--- the use of computers to characterize the molecular components of living things."

-  From the Bioinformatics FAQ at http://bioinformatics.org/faq/

Computational molecular biology, or bioinformatics, draws on the disciplines of biology, mathematics, statistics, physics, chemistry, computer science, and engineering. It provides the computational support for functional genomics, which links the behavior of cells, organisms, and populations to the information encoded in the genomes, as well as for structural genomics. This course is designed to introduce computer science majors to bioinformatics issues and algorithms. A good understanding of general algorithms and data structures, as covered in a 151-like course, is required.

Required Text(s)

	Computational Molecular Biology: An Algorithmic Approach, 1/e Pavel A. Pevzner, 2000. The MIT Press Cambridge, Massachussetts. ISBN 0-26-216197-4
	Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, 1/e Dan Gusfield, 1997. Cambridge University Press New York. ISBN 0-52-158519-8

Additional Requirements

	Students will be required to open and maintain a Chico State Connection (CSC Portal) account.
	Students will be required to open and maintain a WebCT account to access up-to-date on-line calendar of events, current scores, on-line quizzes, etc.

Objectives

1. To become familiar with the fundamental concepts of bioinformatics relative to the computing sciences.
2. To become competent in recognizing what computational molecular biology algorithms are available for specific application areas in bioinformatics.
3. To develop a sufficient understanding of molecular biology concepts necessary to facilitate conversations with other bioinformatics personnel.

Grade Evaluation

This course is designed to give students an equal opportunity of exposure to both Theory and Practice. Students are expected to demonstrate proficiency on both the theoretical and practical aspects of this course.

Theoretical Component  (50%)
	40%		In-Class Quizzes
	30%		Midterm Exam
	30%		Final Exam
Practical Component  (50%)
	50%		Written Homework
	50%		Project(s)

Students are required to earn a C or better in both the Theoretical and the Practical components; otherwise, the minimum of the scores of the two components will be used to calculate the student's final grade.

Final Grades

Final grades shall be expressed as a percentage of the maximum possible score of all evaluated materials. Letter grades will be given according to the following scheme:

Real Interval	Letter Grade	University Definition
[96.25,100.00]	A	Superior Work
[92.50, 96.25)	A-
[88.75, 92.50)	B+	Very Good Work
[85.00, 88.75)	B
[81.25, 85.00)	B-
[77.50, 81.25)	C+	Adequate Work
[73.75, 77.50)	C
[70.00, 73.75)	C-
[66, 70)	D+	Minimally Acceptable Work
[60, 66)	D
[ 0, 60)	F	Unacceptable Work

Note:  It is Dr. J's policy not to assign a final grade of D or D+ to graduate students. Hence,
graduate students with a class standing less than C- (70%) earn a final grade of F.

Attendance/Exams

Attendance will not be checked. However, you are responsible for ALL subject matter and procedural information discussed in class (topics may be covered in the exams). If the instructor is notified beforehand as to why an exam cannot be taken as scheduled (and the reasons are approved and decided to be valid by the instructor), the student may take the exam at an earlier date/time.

The Final Exam is comprehensive.

Absolutely no makeup test will be given for any missed exam. Excused absences will only be considered as defined in the University Catalog.

Assignments and Quizzes

Students are expected to submit all Assignments and Projects to earn a passing grade for the course. Otherwise, the instructors have the option of lowering the student's final grade by at least 1 letter grade.

Quizzes are normally given toward the end of the class period. Quiz schedules will, generally, not be announced. No make-up will be given for missed quizzes, unless the student has sufficient documentation that verifies inability to take the quiz as scheduled. It will be the student's responsibility not to miss any or too many quizzes during the semester.

Grade Disputes

Students have the whole semester to inquire their class standing and to contest any perceived grade discrepancies. You are expected to adhere to the following procedure when resolving disagreements with any given score, grading, or calculated class standing:

1. Submit, in writing, a detailed description of the disagreement in question. This must be submitted within a week after the item in question was announced, posted, or distributed. The document must have the student's signature and the date when the student signed it. There should also be an area where the professor can sign and date the document as to when it was received.

2. The professor will sign and date the said document once it is received. At that time, the professor and student may discuss the discrepancy or an appointment may be made so that both professor and student can review the said disagreement.

3. The professor will make a decision on the matter no later than one (1) week after the discussion in item #2 above. This decision and any related settlement will be made in writing, and a copy of this document will immediately be returned to the student.

Other Matters

Students are responsible for reading and being aware of the following:

• Academic Policies
• Academic Integrity
• Students with Disabilities
• CSU-Chico's Computing Resources P olicy

Dr. Juliano does not hold regular office hours during finals week. However, appointments may be made if necessary (availability based on that week's schedule). Walk-ins are welcome only if his office door is open.

Under no circumstances should students inquire (in person, through the phone, etc.) About their final grades during finals week and the week after. Dr. Juliano will post final grades (for students requesting such) as soon as they are available. If a student wishes to contest any perceived grade discrepancies this late in the semester, the above procedure must be followed; however, all such matters must be settled before final grades are submitted to the Registrar's Office.