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.
Contents
The Courses
BCB410H1F is the undergraduate course code and JTB2020H1S is the course code for graduate students. However the delivery and scope of the courses is very different:
- BCB410 is intended for students in the Bioinformatics and Computational Biology Specialist Program. Therefore I assume that all students are very familiar with a wide variety of computer science related topics and their practical application.
- JTB2020 is designed for students in the Collaborative PhD Program in Bioinformatics and Genome Biology. These students have a wide variety of backgrounds and prior experience. They participate in the Computational Systems Biology Course and go through a number of targeted exercises in applied bioinformatics to add as much material to their knowledge- and skill set as can reasonably be acquired in a single term.
Continue here for the current BCB410 course page ...
Topics
| Hardware |
| High performance computing |
| Cloud computing |
| Systems and Tools |
| Unix |
| Network Configuration |
| Apache |
| MySQL |
| Tools for the bioinformatics lab |
| GBrowse and LDAS |
| Programming |
| IDE (Integrated Development Environment) |
| Regular Expressions |
| Screenscraping |
| Perl |
| BioPerl |
| PHP |
| Relational database principles |
| BioPython |
| Graphical output |
| Autonomous agents |
| 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 |
| SADI Semantic Automated Discovery and Integration |
| CGI |
| Statistics |
| Pattern discovery |
| Correlation |
| Clustering methods |
| Cluster metrics |
| The Map Equation |
| Machine learning |
| R |
| - R plotting |
| - R programming |
| - R EDA |
| - R regression |
| - R PCA |
| - R Clustering |
| - R Classification |
| - R hypothesis testing |
| - Bioconductor |
| Applications |
| Data integration |
| Text mining |
| HMMER |
| High-throughput sequencing |
| Functional annotation |
| Microarray analysis |
