CIS325 Bioinformatics II
Instructor: Falcon Chu
Email: helpdesk@ksi.edu
Phone: 847 679-3135
Fax: 847 679-3166
Course Description
This course is a continuation of Bioinformatics I. In this course, students will be raised to a higher level of Perl programming in bioinformatics, including parsing FASTA, reading GenBank files and processing BLAST output files. Students will also be guided to more advanced programming techniques, including advanced data structures, modules and object-oriented programming in Perl. The only prerequisite for the course is Bioinformatics I, or
equivalent training at another institution.
Textbook
Text: Beginning Perl for Bioinformatics, by James D. Tisdall
Publisher: O'Reilly & Associates, Inc (ISBN 0-596-00080-4)
Mastering Perl for Bioinformatics, by James D. Tisdall
Publisher: O'Reilly & Associates, Inc (ISBN 0-596-00307-2)
Mastering Perl/Tk, by Steve Lidie and Nancy Walsh
Publisher: O'Reilly & Associates, Inc (ISBN 1-56592-716-8)
Hardware and Software
The essential software for the course is open-source and should be installed on an IBM-compatible PC under Windows 98, NT, ME, 2000 or XP. In addition, these online documents are available for reference:
- ActiveState's Perl, v. 5.8.6 or higher versions built for MSWin32-x86-multithread (www.perl.org)
- CPAN (Comprehensive Perl Archive Network) script v. 1.01 and CPAN.pm v.1.7601 (www.cpan.org)
- ActiveState's Perl/Tk v. 804.027 (www.PerlTk.org), a document that can be downloaded from CPAN
Course Requirements
Successful completion of the course requires writing five programming assignments and finishing four tests. The programming assignments will be 50% of the grade, the tests 40% and class participation 10%.
Students must submit assignments and projects by the due date in order to
avoid losing credit for lateness. Students will receive an Incomplete if
they fail to submit two or more of the assignments and projects and miss
either the mid-term or final exam. Students will fail the course if they
attend less than half of the classes or fail to submit three or more
assignments and projects. Students receiving an Incomplete will have 15 days
to complete all unfinished work. Receiving an Incomplete at the end of the
term will preclude receiving more than a "B" for the final grade.
Each student will submit original work in order to receive credit for the
course. Please consult the KSI Policy on Academic Dishonesty. Team members
are expected to cooperate only with members of their own team. Programs are
to be run on an IBM PC or similar products such as are available in the
computing labs, using the ActiveState's Perl software already indicated.
Perl and Perl/Tk source programs with the extension .pl and Perl module
program with .pm are to be submitted as an email attachment for each project
assigned. Students should keep backup copies of each program.
Course Topics:
- GenBank
- Protein Data Bank
- BLAST
- Lab/Seminar
- Modular Programming with Perl
- Data Structures and String Algorithms
- Lab/Seminar
- Object-Oriented Programming in Perl - 1
- Object-Oriented Programming in Perl - 2
- Lab/Seminar
- Sequence Formats and Inheritances - 1
- Sequence Formats and Inheritances - 2
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