Syllabus  -  Introduction to Bioinformatic Computation Course

BIPG 6100/8100 - Introduction to Bioinformatic Computation
Syllabus – Spring 2013 *

All classes are held in the BPG computer classroom, HEB 127, beginning Monday, January 14, 2013

 Objectives:

The purpose of this course is to introduce students to use of computers to solve biological problems.  The following will be included:

1) Use of the LINUX operating system
2) Use of PERL programming languagefor bioinformatic analysis
3) Use of bioinformatic programs on a desktop computer (local, BLAST, REPEATMASKER, CLUSTALW)
4) Database management (generation of Exon-Intron Database

Course Coordinator:
Alexei Fedorov, Ph.D.
Office: Room 12 RHC
Associate Professor
Head of Bioinformatics Lab
Department of Medicine
Tel: (419)‑383‑5270
Fax: (419)‑383‑3102
Email: alexei.fedorov@utoledo.edu

 

WEEK 1 (3h)

Introduction to computer science for biological tasks.  What biologists should know about computers.
Introduction to the LINUX platform.
Working in a LINUX environment, part 1: basic UNIX commands. (ls, cat, pwd, cd, mkdir,  rm, mv, cp, more, less, chmod etc…).

 

WEEK 2 (3h)

Working in a LINUX environment, part 2: a) working with large text databases;
      b) simple programming in UNIX (pipelines; grep, sort, vi).
Introduction to PERL.
Practicing in PERL 1:  variables and arrays; operators for strings and arrays; opening files and printing into files.

 

WEEK 3 (3h)

Introduction to PERL continued.
Practicing in PERL :  regular expressions.
Practicing in PERL:  more about regular expressions.
Substitutions, transliteration, match variables

 

WEEK 4 (3h)

Control structures (if, else, elsif, unless); Loops (for, foreach, while); Operators: last, next; Blocks.
 

WEEK 5 (3h)

Associative arrays; multidimensional arrays, arrays of hashes.

 

WEEK 6 (3h)

Local BLAST: installation from NCBI; choosing parameters for blast; preparation of local databases for BLAST; running the program.
Invoking BLAST inside Perl scripts (system calls).
Analysis of BLAST output using Perl scripts.

 

WEEK 7 (3h)

Other useful local programs and databases: RepeatMasker program, Repeat Database;
     ClustalW for multiple alignments.

 

WEEK 8 (3h)

Creation of Exon-Intron Database from GenBank Current release
Make.EID.pl package
Downloading GenBank database
Running Make.EID.pl

 

WEEK 9 (3h)

2-D genomic gel electrophoresis in silico.

 

WEEK 10 (3h)

Algorithm optimization for sequence analysis.
Comparisons of vast genomic sequences.
Designing a new program.

 

WEEK 11 (3h)

Random number generator; Monte Carlo simulations.

 

WEEK 12 (3h)

BioPerl; subroutines, packages, modules, and objects.

 

WEEK 13 (3h)

Other computer languages (includes 2h lecture (invited speakers) and 2h lab )

 

WEEK 14 (3h)

Database management, SQL language (includes 2h lecture (invited speakers) and 2h lab)

 

WEEK 15 (3h)

Practicing with object-oriented programming.

 

WEEK 16 (3h)

Exams

 

 

* Exam weeks are not included