Syllabus, Practical Bionformatics Lab, Spring 2005

BIOS 499/599, Practical Bioinformatics Lab
Spring 2005
Gale Life Sciences, #208

Course Syllabus

Course Description:

Students taking this practical laboratory course will learn the skills and basic concepts necessary for bioinformatics research. Each three-hour lab period will consist of a short lecture followed by hands-on exercises on the computer. Perl will be the programming language, but emphasis will be placed on generic concepts whenever possible.

Students will gain the tools to work efficiently with large data sets on the various platforms in current use. A successful student will be able to use a wide range of bioinformatics tools with genuine understanding. The specific topics to be covered are:

• Basic Programming
• Control Structures
• Data Structures (Scalars, Arrays, Hashes)
• File Handling
• Subroutines, Modules and Libraries
• Debugging
• Perl Syntax
• Operating System Fundamentals (OS X, Linux/UNIX)
• Pipes
• Computer Science Topics
• Open Source/Open Access
• Run-Time Measurement (Big O)
• Regular Expressions and String Matching
• Object Orientation
• Cluster Computing
• Algorithms

This is a large number of topics, so the focus will be to introduce the essential vocabulary and concepts to allow a biologist to interpret and use bioinformatic literature and tools. Motivated students will leave prepared to explore current bioinformatic research topics according to their own interests and goals.

Prerequisites:

The only prerequisite is a high level of interest in biological applications of computer science and programming. An ISU e-mail account is required, since all course correspondence will be sent using this account.

This course has no strict prerequisites, but a certain level of computer literacy is expected. This includes familiarity with essential protocols like FTP and SSH/Telnet and a fundamental grasp of the client/server model of computing. Motivation to learn independently and make full use of Internet, written and interpersonal resources is absolutely essential.

Suggested Texts:

Perl in a Nutshell, 2nd Edition
    By Stephen Spainhour, Ellen Siever, Nathan Patwardhan
    2nd Edition June 2002
    Series: In a Nutshell
    ISBN: 0-596-00241-6
    800 pages, $39.95 US

Bioinformatics, Biocomputing and Perl: An Introducton to Bioinformatic Computing Skills and Practice.
     by Michael Moorhouse and Paul Barry
     1st Edition, 2004
     Wiley, 480 pages, $75.00

Many appropriate references will be suggested on the first day of class. You may also discover your own reference materials, printed or web-based.

Grading:
This course will include students with a wide range of programming skills. The course will be graded most heavily on participation, the quality of comments in your code and on presentation of your work. A short graded assignment or presentation will be due every class period as evidence of active participation. Programming is (contrary to stereotypes) a social and linguistic exercise, so talking and ethical code-sharing is encouraged.

Feb. 1 addendum: As is typical for laboratory courses, regular attendance is absolutely required. Three unexcused absences during one semester will result in a failing grade. This course is entirely experiential by design and it is nearly impossible to make up missed classes.

Class Communications: All electronic communications will take place through your official ISU address, no exceptions. If you use another account more regularly, there is a clever trick that will forward any mail to your official account to your preferred address. This secret will be revealed the first class meeting.

Academic Integrity:
All applicable Idaho State University policies regarding academic integrity will be honored by all participants. See your official catalog, student handbook or the ISU web site for details. This course allows group-learning, but respects individual accountability and credit-where-credit-is-due. Ethical re-use of code from other sources is encouraged except during testing situations. Proper citation of all sources for borrowed code is mandatory (and it's the right thing to do).