Aug 28
Discussion:
Course introduction
Lab:
Pretest and tutorials;
Miniproject: What is bioinformatics?
Sep 2
Discussion:
Introduction to web searching
Lab:
Webexercise;
Miniproject due
Sep 4
Unit 1: Databases
Discussion:
Searching databases
Lab:
Webexercise2;
Molecular databases;
Project intro: BLAST
Sep 9
Discussion:
Database structure & design
useful sites
Lab:
Application service providers;
Inside BLAST.
Sep 11
Discussion:
Algorithms, heuristics, informatics
Lab:
Multiple sequence alignment;
BLAST project due
Sep 16
Discussion:
Project: Molecular parasitology application
Lab:
Online bioinformatics tools;
MSA data format
Sep 18
Discussion:
Documenting a computational experiment
Lab:
Organizing and analyzing results
Sep 23
Discussion:
Presentation project results
Lab:
Interpreting sequence data
Sep 25
Unit 2: Genomics
Discussion:
Overview; Genome data controversy
Lab:
Genomic DNA sequencing
Sep 30
Discussion:
Gene finding, feature mapping
Lab:
CAP3, EMBOSS and GrailEXP
Oct 2
Discussion:
Genome structure, function and evolution
Lab:
Project: Genome mapping and comparison
Oct 7
Discussion:
Presentation genome project results
Lab:
Genome annotation, PERL and BIOPERL
Oct 9
Unit 3: Genetics
Discussion:
Polymorphisms; linkage analysis
Lab:
Mapping disease genes; microarrays
Oct 14
Discussion:
Applications of microarrays
Lab:
Project: Expression studies of disease and evolution
Oct 16
Discussion:
Ethical issues in bioinformatics
Lab:
TBA
Oct 21
Midsemester
problem set
Oct 23
Discussion:
Expression analysis project presentation
Lab:
Expression analysis software
Oct 28
Unit 4: Phylogenetics
Discussion:
Tree building by parsimony & maximum likelihood
Lab:
Multiple sequence alignment
Oct 30
Discussion:
Phylogenetic analysis
Lab:
Biology Workbench tree tools
Nov 4
Discussion:
Project: Molecular Evaluation of Diversity
Lab:
Phylogenetic identification of unknown DNAs
Nov 6
Discussion:
PHYLIP
Lab:
Phylogeny project presentation
Nov 11
Unit 5: Prot. Structure
Discussion:
Classifying proteins; patterns, motifs & profiles
Lab:
SwissProt & PDB databases
Nov 13
Discussion:
3D structure determination;
Project: Protein structure modeling
Lab:
Modeling software and sites
Nov 18
Discussion:
Protein folding
Lab:
Secondary structure prediction
Nov 20
Discussion:
Structural genomics
Lab:
Structure/function inference;
Presentation of project results
Nov 25
Unit 6: Networks
Discussion:
No Class
Lab:
No Lab
THANKSGIVING BREAK
Dec 2
Discussion:
Drug design, data mining
Lab:
Metabolic databases; data mining methods
Making connections
Dec 4
Discussion:
Metabolic pathways, signaling networks
Lab:
Project: Data mining
Dec 9
Discussion:
Proteomics; Protein-protein interactions
Lab:
Complex data sets
Dec 11
Discussion:
Clustering software; self-organizing maps
Lab:
Data mining project due
Dec 16
Project proposals
due: 5:00 p.m.
ANNOUNCEMENTS