Applied Bioinformatics Main Page

Applied Bioinformatics

Welcome to the Applied Bioinformatics Course Wiki.

These wiki pages are provided to coordinate information, activities and projects in the applied bioinformatics courses taught by Boris Steipe at the University of Toronto. If you are not one of my students, you can still browse this site, however only users with a login account can edit or contribute or edit material. If you are here because you are interested in general aspects of bioinformatics or computational biology, you may want to review the Wikipedia article on bioinformatics, or visit Wikiomics. Contact boris.steipe(at)utoronto.ca with any questions you may have.

The Courses

This material is variably being used in my undergraduate courses BCH441 (Bioinformatics), BCB410 (Applied Bioinformatics), BCB420 (Computational Systems Biology), their graduate course cognates BCH1441 and JTB2020, and other workshops I teach.

 

Continue here for the current BCB410H course page ...

 

Continue here for guidelines on BCB330Y and BCB430Y projects with me ...

 

Topics

Hardware High performance computing Cloud computing   Systems and Tools Unix Unix system administration Unix commandline tools Unix automation Program installation wget Network Configuration Apache MySQL Tools for the bioinformatics lab GBrowse and LDAS   Programming Software Development (in a small-scale research context) SPN (Structured Process Notation) IDE (Integrated Development Environment) Regular Expressions Screenscraping Perl Perl basic programming Perl hash example Perl LWP example Perl MySQL introduction Perl OBO parser Perl basic programming Perl programming exercises 1 Perl programming exercises 2 Perl programming Data Structures Perl references Perl simulation Regular Expressions Perl: Object oriented programming Perl: Ugly programming BioPerl PHP Data modelling BioPython Graphical output Autonomous agents CVS / Git Algorithms General Algorithms Optimization   Algorithms on Sequences Dynamic Programming Multiple Sequence Alignment Genome Assembly   Algorithms on Structures Docking Protein Structure Prediction   Algorithms on Trees Computing with trees   Algorithms on Networks Network metrics Dijkstras Algorithm Floyd Warshall Algorithm Communication and collaboration MediaWiki HTML essentials HTML 5 CSS SADI and SHARE - a Semantic Web Service framework CGI   Statistics Pattern discovery Correlation Clustering methods Cluster quality metrics The Map Equation Machine learning Information theory R Introductory tutorial to R R plotting R programming R EDA R regression R PCA R Clustering R Gene expression clustering R Classification R hypothesis testing Bioconductor Regular Expressions Bayesian inference   Applications BLAST scripting Chimera programming Biological data access and integration Text mining HMMER High-throughput sequencing Functional annotation Microarray analysis

Resources

Course related

• Netiquette for the Group mailing list

Contents related

• Chimera
• A Stereo Vision tutorial
• Workshops taught elsewhere