Difference between revisions of "Applied Bioinformatics Main Page"
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==Topics== | ==Topics== | ||
| − | <table width=" | + | <table width="40%"><tr><td> |
| − | <tr | + | |
| − | <tr class="s1"><td>High performance computing <!-- (... at the bench: GPUs, FPGAs, Clusters) --></td></tr> | + | ===Hardware=== |
| − | <tr class="s2"><td>Cloud computing</td></tr> | + | <table width="90%" align="left"> |
| + | <tr class="s1"><td class="l1">High performance computing <!-- (... at the bench: GPUs, FPGAs, Clusters) --></td></tr> | ||
| + | <tr class="s2"><td class="l1">Cloud computing</td></tr> | ||
</table> | </table> | ||
| − | <table width=" | + | ===Systems and Tools=== |
| − | <tr class=" | + | <table width="90%" align="left"> |
| − | + | <tr class="s1"><td class="l1">[[Unix]]</td></tr> | |
| − | <tr class="s2"><td>[[Network Configuration]]</td></tr> | + | <tr class="s2"><td class="l1">[[Network Configuration]]</td></tr> |
| − | <tr class="s1"><td>[[Apache]]</td></tr> | + | <tr class="s1"><td class="l1">[[Apache]]</td></tr> |
| − | <tr class="s2"><td>[[MySQL]]</td></tr> | + | <tr class="s2"><td class="l1">[[MySQL]]</td></tr> |
| − | <tr class="s1"><td>[[Tools for the bioinformatics lab]]</td></tr> | + | <tr class="s1"><td class="l1">[[Tools for the bioinformatics lab]]</td></tr> |
| − | <tr class="s2"><td>[[GBrowse|GBrowse and LDAS]]</td></tr> | + | <tr class="s2"><td class="l1">[[GBrowse|GBrowse and LDAS]]</td></tr> |
</table> | </table> | ||
| − | <table width=" | + | ===Programming=== |
| − | <tr class=" | + | <table width="90%" align="left"> |
| − | + | <tr class="s1"><td class="l1">[[IDE|IDE (Integrated Development Environment)]]</td></tr> | |
| − | <tr class="s2"><td>[[Regular Expressions]]</td></tr> | + | <tr class="s2"><td class="l1">[[Regular Expressions]]</td></tr> |
| − | <tr class="s1"><td>[[Screenscraping]]</td></tr> | + | <tr class="s1"><td class="l1">[[Screenscraping]]</td></tr> |
| − | <tr class="s2"><td>[[Perl]]</td></tr> | + | <tr class="s2"><td class="l1">[[Perl]]</td></tr> |
| − | <tr class="s1"><td>[[BioPerl]]</td></tr> | + | <tr class="s1"><td class="l1">[[BioPerl]]</td></tr> |
| − | <tr class="s2"><td>[[PHP]]</td></tr> | + | <tr class="s2"><td class="l1">[[PHP]]</td></tr> |
| − | <tr class="s1"><td>[[Relational database principles]]</td></tr> | + | <tr class="s1"><td class="l1">[[Relational database principles]]</td></tr> |
| − | <tr class="s2"><td>BioPython <!-- (scope, highlights, installation, use, support) --></td></tr> | + | <tr class="s2"><td class="l1">BioPython <!-- (scope, highlights, installation, use, support) --></td></tr> |
| − | <tr class="s1"><td>Graphical output <!-- (PNG and SVG) --></td></tr> | + | <tr class="s1"><td class="l1">Graphical output <!-- (PNG and SVG) --></td></tr> |
| − | <tr class="s2"><td>[[Autonomous agents]]</td></tr> | + | <tr class="s2"><td class="l1">[[Autonomous agents]]</td></tr> |
</table> | </table> | ||
| − | <table width=" | + | ===Algorithms=== |
| − | <tr class="sh"><td>Algorithms on Sequences</td></tr> | + | <table width="90%" align="left"> |
| − | <tr class="s1"><td>[[Dynamic Programming]]</td></tr> | + | <tr class="sh"><td class="l1">Algorithms on Sequences</td></tr> |
| − | <tr class="s2"><td>[[Multiple Sequence Alignment]]</td></tr> | + | <tr class="s1"><td class="l2">[[Dynamic Programming]]</td></tr> |
| − | <tr class="s1"><td>[[Genome Assembly]]</td></tr> | + | <tr class="s2"><td class="l2">[[Multiple Sequence Alignment]]</td></tr> |
| − | <tr class="sh"><td>Algorithms on Structures</td></tr> | + | <tr class="s1"><td class="l2">[[Genome Assembly]]</td></tr> |
| − | <tr class="s1"><td>[[Docking]]</td></tr> | + | |
| − | <tr class="s2"><td>Protein Structure Prediction <!-- ''ab initio'' --></td></tr> | + | <tr><td class="sp"> </td></tr> |
| − | <tr class="sh"><td>Algorithms on Trees</td></tr> | + | |
| − | <tr class="s1"><td>Computing with trees <!-- Bayesian approaches for phylogenetic trees, tree comparison) --></td></tr> | + | <tr class="sh"><td class="l1">Algorithms on Structures</td></tr> |
| − | <tr class="sh"><td>Algorithms on Networks</td></tr> | + | <tr class="s1"><td class="l2">[[Docking]]</td></tr> |
| − | <tr class="s1"><td>Network metrics <!-- (Degree distributions, Centrality metrics, other metrics on topology, small-world- vs. random-geometric controversy) --></td></tr> | + | <tr class="s2"><td class="l2">Protein Structure Prediction <!-- ''ab initio'' --></td></tr> |
| − | <tr class="s2"><td>[[Dijkstras Algorithm]]</td></tr> | + | |
| − | <tr class="s1"><td>[[Floyd Warshall Algorithm]]</td></tr> | + | <tr><td class="sp"> </td></tr> |
| + | |||
| + | <tr class="sh"><td class="l1">Algorithms on Trees</td></tr> | ||
| + | <tr class="s1"><td class="l2">Computing with trees <!-- Bayesian approaches for phylogenetic trees, tree comparison) --></td></tr> | ||
| + | |||
| + | <tr><td class="sp"> </td></tr> | ||
| + | |||
| + | <tr class="sh"><td class="l1">Algorithms on Networks</td></tr> | ||
| + | <tr class="s1"><td class="l2">Network metrics <!-- (Degree distributions, Centrality metrics, other metrics on topology, small-world- vs. random-geometric controversy) --></td></tr> | ||
| + | <tr class="s2"><td class="l3">[[Dijkstras Algorithm]]</td></tr> | ||
| + | <tr class="s1"><td class="l3">[[Floyd Warshall Algorithm]]</td></tr> | ||
</table> | </table> | ||
| − | <table width=" | + | ===Communication and collaboration=== |
| − | <tr class=" | + | <table width="90%" align="left"> |
| − | + | <tr class="s1"><td class="l1">[[MediaWiki]]</td></tr> | |
| − | <tr class="s2"><td>[[HTML essentials]]</td></tr> | + | <tr class="s2"><td class="l1">[[HTML essentials]]</td></tr> |
| − | <tr class="s1"><td>[[HTML 5]]</td></tr> | + | <tr class="s1"><td class="l1">[[HTML 5]]</td></tr> |
| − | <tr class="s2"><td>[[SADI|SADI Semantic Automated Discovery and Integration]]</td></tr> | + | <tr class="s2"><td class="l1">[[SADI|SADI Semantic Automated Discovery and Integration]]</td></tr> |
| − | <tr class="s1"><td>[[CGI]]</td></tr> | + | <tr class="s1"><td class="l1">[[CGI]]</td></tr> |
</table> | </table> | ||
| − | <table width=" | + | ===Statistics=== |
| − | <tr class=" | + | <table width="90%" align="left"> |
| − | + | <tr class="s1"><td class="l1">[[Pattern discovery]]</td></tr> | |
| − | <tr class=" | + | <tr class="s2"><td class="l1">Correlation <!-- (Covariance matrices and their interpretation, application to large problems, collaborative filtering, MIC and MINE) --></td></tr> |
| − | <tr class="s1"><td>Clustering methods <!-- (Algorithms and choice (including: hierarchical, model-based and partition clustering, graphical methods (MCL), flow based methods (RRW) and spectral methods). Implementation in R if possible) --></td></tr> | + | <tr class="s1"><td class="l1">Clustering methods <!-- (Algorithms and choice (including: hierarchical, model-based and partition clustering, graphical methods (MCL), flow based methods (RRW) and spectral methods). Implementation in R if possible) --></td></tr> |
| − | <tr class=" | + | <tr class="s2"><td class="l1">Cluster metrics <!-- (Cluster quality metrics (Akaike, BIC)–when and how) --></td></tr> |
| − | <tr class=" | + | <tr class="s1"><td class="l1">[[Map equation|The Map Equation]] </td></tr> |
| − | <tr class=" | + | <tr class="s2"><td class="l1">Machine learning <!-- (Classification problems: Neural Networks, HMMs, SVM..) --></td></tr> |
| − | <tr class=" | + | <tr class="s1"><td class="l1">[[R]]</td></tr> |
| − | <tr class=" | + | <tr class="s2"><td class="l2">R plotting</td></tr> |
| − | <tr class=" | + | <tr class="s1"><td class="l2">[[R programming]]</td></tr> |
| − | <tr class=" | + | <tr class="s2"><td class="l2">R EDA</td></tr> |
| − | <tr class=" | + | <tr class="s1"><td class="l2">R regression</td></tr> |
| − | <tr class=" | + | <tr class="s2"><td class="l2">R PCA</td></tr> |
| − | <tr class=" | + | <tr class="s1"><td class="l2">R Clustering</td></tr> |
| − | <tr class=" | + | <tr class="s2"><td class="l2">R Classification <!-- Phrasing inquiry as a classification problem, dealing with noisy data, machine learning approaches to classification, implementation in R) --></td></tr> |
| − | <tr class=" | + | <tr class="s1"><td class="l2">R hypothesis testing</td></tr> |
| − | <tr class=" | + | <tr class="s2"><td class="l2">[[Bioconductor]]</td></tr> |
</table> | </table> | ||
| + | ===Applications=== | ||
| + | <table width="90%" align="left"> | ||
| + | <tr class="s1"><td class="l1">[[Data integration]] <!-- Add BioMart: Biodata integration, and data-mining of complex, related, descriptive data --></td></tr> | ||
| + | <tr class="s2"><td class="l1">Text mining <!-- (Use cases, tasks and metrics, taggers, vocabulary mapping, Practicals: R-support, Python/Perl support, others...) --></td></tr> | ||
| + | <tr class="s1"><td class="l1">[[HMMER]]</td></tr> | ||
| + | <tr class="s2"><td class="l1">High-throughput sequencing</td></tr> | ||
| + | <tr class="s1"><td class="l1">Functional annotation <!-- GFF --></td></tr> | ||
| + | <tr class="s2"><td class="l1">Microarray analysis <!-- (... in R: differential expression and multiple testing; Loading and normalizing data, calculating differential expression, LOWESS, the question of significance, FWERs: Bonferroni and FDR; SAM and LIMMA) --></td></tr> | ||
| + | </table> | ||
| + | </td></tr></table> | ||
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Revision as of 03:17, 19 September 2012
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
Systems and Tools
Programming
Algorithms
Communication and collaboration
Statistics
Applications
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