Selected Topics in Zoology (Section 28329):
Introduction to Bioinformatics and Genomics
Introduction to Bioinformatics and Genomics
BIOL Z620 Spring 2013
Course description
BIOL Z620 ItBG
Lecture times and locations
Mon, Wed 12:45p-2:15p, Lindley Hall (LH) 030
Tentative schedule (click the icon for a 
version)
| DAY | DATE | LECTURE | TOPIC | LECTURER | Mon | Jan 7 | 1.1 | Orientation Introduction to informatics and computation in biology | Volker Brendel |
| Wed | Jan 9 | 1.2 | Introduction to genomic approaches in biology The CTFR gene as a case study | Irene Newton |
| Mon | Jan 14 | 2.1 | Perl for bioinformatics scripting: Introduction (Learning Perl, Chapter 1) Scalar Data (Learning Perl, Chapter 2) Scripting assignment 1 | Irene Newton |
| Wed | Jan 16 | 2.2 | Perl for bioinformatics scripting: Lists and Arrays (Learning Perl, Chapter 3) Hashes (Learning Perl, Chapter 5) Scripting assignment 2 | Irene Newton |
| Mon | Jan 21 | MLK Jr. Day - no class | n/a | |
| Wed | Jan 23 | 2.3 | Perl for bioinformatics scripting: Subroutines (Learning Perl, Chapter 4) Scripting assignment 3 | Irene Newton |
| Mon | Jan 28 | 2.4 | Perl for bioinformatics scripting: I/O Basics (Learning Perl, Chapter 6) Filehandles and File Tests (Learning Perl, Chapter 11) Scripting assignment 4 | Irene Newton |
| Wed | Jan 30 | 2.5 | Perl for bioinformatics scripting: Regular Expressions (Learning Perl, Chapters 7-9) Scripting assignment 5 | Irene Newton |
| Mon | Feb 4 | 3.1 | Sequence alignment Reading assignment 1 | Volker Brendel |
| Wed | Feb 6 | 3.2 | Sequence alignment | Volker Brendel |
| Mon | Feb 11 | 4.1 | Sequence alignment | Volker Brendel |
| Wed | Feb 13 | 4.2 | Sequence alignment | Volker Brendel |
| Mon | Feb 18 | 4.3 | Sequence alignment | Irene Newton |
| Wed | Feb 20 | 4.4 | Sequence alignment | Volker Brendel |
| Mon | Feb 25 | 5.1 | Molecular Phylogeny: Reading assignment 3 | Volker Brendel |
| Wed | Feb 27 | 5.2 | Molecular Phylogeny: Parsimony and Distance Matrix Methods | Volker Brendel |
| Mon | Mar 4 | 5.3 | Molecular Phylogeny: Project-related computational laboratory A list of Web-servers for molecular phylogeny analyses Mobyle @ Pasteur Data analysis assignment 2 | Volker Brendel |
| Wed | Mar 6 | 5.4 | Genome assembly and annotation: Project-related computational laboratory Data analysis assignment 3 | Instructors |
| Mon | Mar 11 | SPRING BREAK - no class | n/a | |
| Wed | Mar 13 | SPRING BREAK - no class | n/a | |
| Mon | Mar 18 | 6.1 | Gene expression analyses: Reading assignment 6 | Irene Newton |
| Wed | Mar 20 | 6.2 | Gene expression analyses: | Irene Newton |
| Mon | Mar 25 | 6.3 | Gene expression analyses: Project-related computational laboratory Data analysis assignment 3 | Instructors |
| Wed | Mar 27 | 7.1 | Protein structure: Secondary Structures (Understanding Bioinformatics, Chapter 5) Reading assignment 7: Review of Protein Structure Prediction Resources: A listing of protein structure prediction servers | Volker Brendel |
| Mon | April 1 | 7.2 | Examples of Perl usage for protein structure data: Parsing PDB files Processing of program output (Requires STRIDE, available via ftp) | Volker Brendel |
| Wed | April 3 | 7.3 | Protein structure: Project-related computational laboratory Data analysis assignment 4 | Instructors |
| Mon | April 8 | 8.1 | Back to Perl I: Putting bits and pieces together for protein secondary structure analyses | Volker Brendel |
| Wed | April 10 | 8.2 | Back to Perl II: Using BioPerl | Volker Brendel |
| Mon | April 15 | 8.3 | Special topics - Metabolic reconstruction Reading assignment 9 | Irene Newton |
| Wed | April 17 | 8.4 | Special topics - Metabolic reconstruction: Project-related computational laboratory Data analysis assignment 6 | Instructors |
| Mon | April 22 | 9.1 | Final project preparation | Instructors |
| Wed | April 24 | 9.2 | Final project preparation | Instructors |
| Wed | May 1 | 11:59pm | Final Projects due | students |