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== The Courses == | == 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. | |
| − | + | {{Vspace}} | |
| − | |||
<div class="alert"> | <div class="alert"> | ||
| − | Continue [[ | + | Continue [[BCB410|'''here''']] for the current BCB410H course page ... |
</div> | </div> | ||
| + | {{Vspace}} | ||
| + | |||
| + | <div class="alert"> | ||
| + | Continue [[BCB330|'''here''']] for guidelines on BCB330Y and BCB430Y projects with me ... | ||
| + | </div> | ||
| + | |||
| + | |||
| + | {{Vspace}} | ||
==Topics== | ==Topics== | ||
| − | <table width=" | + | <table width="60%"><tr><td class="l1"> </td><td> |
===Hardware=== | ===Hardware=== | ||
| − | <table width=" | + | <table width="100%"> |
<tr class="s1"><td class="l1">High performance computing <!-- (... at the bench: GPUs, FPGAs, Clusters) --></td></tr> | <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> | <tr class="s2"><td class="l1">Cloud computing</td></tr> | ||
| + | <tr><td class="sp"> </td></tr> | ||
</table> | </table> | ||
| + | ===Systems and Tools=== | ||
| + | <table width="100%"> | ||
| + | |||
| + | <tr class="s1"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[Unix]] | ||
| + | <div class="mw-collapsible-content"> | ||
| + | <table width="100%"><tr class="s2"><td class="l2">[[Unix system administration]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s1"><td class="l2">[[Unix commandline tools]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s2"><td class="l2">[[Unix automation]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s1"><td class="l2">[[Program installation]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s2"><td class="l2">[[wget]]</td></tr></table> | ||
| + | </div> | ||
| + | </td></tr> | ||
| − | |||
| − | |||
| − | |||
<tr class="s2"><td class="l1">[[Network Configuration]]</td></tr> | <tr class="s2"><td class="l1">[[Network Configuration]]</td></tr> | ||
<tr class="s1"><td class="l1">[[Apache]]</td></tr> | <tr class="s1"><td class="l1">[[Apache]]</td></tr> | ||
| Line 45: | Line 62: | ||
<tr class="s1"><td class="l1">[[Tools for the bioinformatics lab]]</td></tr> | <tr class="s1"><td class="l1">[[Tools for the bioinformatics lab]]</td></tr> | ||
<tr class="s2"><td class="l1">[[GBrowse|GBrowse and LDAS]]</td></tr> | <tr class="s2"><td class="l1">[[GBrowse|GBrowse and LDAS]]</td></tr> | ||
| + | <tr><td class="sp"> </td></tr> | ||
</table> | </table> | ||
| − | |||
===Programming=== | ===Programming=== | ||
| − | <table width=" | + | <table width="100%" > |
| + | <tr class="s1"><td class="l1">[[Software Development|Software Development <small>(in a small-scale research context)</small>]]</td></tr> | ||
| + | <tr class="s2"><td class="l1">[[SPN|SPN <small>(Structured Process Notation)</small>]]</td></tr> | ||
<tr class="s1"><td class="l1">[[IDE|IDE (Integrated Development Environment)]]</td></tr> | <tr class="s1"><td class="l1">[[IDE|IDE (Integrated Development Environment)]]</td></tr> | ||
<tr class="s2"><td class="l1">[[Regular Expressions]]</td></tr> | <tr class="s2"><td class="l1">[[Regular Expressions]]</td></tr> | ||
<tr class="s1"><td class="l1">[[Screenscraping]]</td></tr> | <tr class="s1"><td class="l1">[[Screenscraping]]</td></tr> | ||
| − | <tr class="s2"><td class="l1">[[Perl]]</td></tr> | + | |
| + | <tr class="s2"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[Perl]] | ||
| + | <div class="mw-collapsible-content"> | ||
| + | <table width="100%"><tr class="s1"><td class="l2">[[Perl basic programming]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s2"><td class="l2">[[Perl hash example]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s1"><td class="l2">[[Perl LWP example]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s2"><td class="l2">[[Perl MySQL introduction]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s1"><td class="l2">[[Perl OBO parser]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s2"><td class="l2">[[Perl basic programming]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s1"><td class="l2">[[Perl programming exercises 1]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s2"><td class="l2">[[Perl programming exercises 2]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s1"><td class="l2">[[Perl programming Data Structures]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s2"><td class="l2">[[Perl references]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s1"><td class="l2">[[Perl simulation]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s2"><td class="l2">[[Regular Expressions]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s1"><td class="l2">[[Perl: Object oriented programming]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s2"><td class="l2">[[Perl: Ugly programming]]</td></tr></table> | ||
| + | </div> | ||
| + | </td></tr> | ||
| + | |||
<tr class="s1"><td class="l1">[[BioPerl]]</td></tr> | <tr class="s1"><td class="l1">[[BioPerl]]</td></tr> | ||
<tr class="s2"><td class="l1">[[PHP]]</td></tr> | <tr class="s2"><td class="l1">[[PHP]]</td></tr> | ||
| − | <tr class="s1"><td class="l1">[[ | + | <tr class="s1"><td class="l1">[[Data modelling]]</td></tr> |
<tr class="s2"><td class="l1">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 class="l1">Graphical output <!-- (PNG and SVG) --></td></tr> | <tr class="s1"><td class="l1">Graphical output <!-- (PNG and SVG) --></td></tr> | ||
<tr class="s2"><td class="l1">[[Autonomous agents]]</td></tr> | <tr class="s2"><td class="l1">[[Autonomous agents]]</td></tr> | ||
| + | <tr class="s1"><td class="l1">CVS / Git</td></tr> | ||
| + | |||
</table> | </table> | ||
| + | ===Algorithms=== | ||
| + | <table width="100%" > | ||
| + | <tr class="sh"><td class="l1">General Algorithms</td></tr> | ||
| + | <tr class="s1"><td class="l2">[[Optimization]]</td></tr> | ||
| + | |||
| + | <tr><td class="sp"> </td></tr> | ||
| − | |||
| − | |||
<tr class="sh"><td class="l1">Algorithms on Sequences</td></tr> | <tr class="sh"><td class="l1">Algorithms on Sequences</td></tr> | ||
<tr class="s1"><td class="l2">[[Dynamic Programming]]</td></tr> | <tr class="s1"><td class="l2">[[Dynamic Programming]]</td></tr> | ||
| Line 88: | Line 132: | ||
<tr class="s1"><td class="l3">[[Floyd Warshall Algorithm]]</td></tr> | <tr class="s1"><td class="l3">[[Floyd Warshall Algorithm]]</td></tr> | ||
</table> | </table> | ||
| − | |||
===Communication and collaboration=== | ===Communication and collaboration=== | ||
| − | <table width=" | + | <table width="100%" > |
<tr class="s1"><td class="l1">[[MediaWiki]]</td></tr> | <tr class="s1"><td class="l1">[[MediaWiki]]</td></tr> | ||
<tr class="s2"><td class="l1">[[HTML essentials]]</td></tr> | <tr class="s2"><td class="l1">[[HTML essentials]]</td></tr> | ||
<tr class="s1"><td class="l1">[[HTML 5]]</td></tr> | <tr class="s1"><td class="l1">[[HTML 5]]</td></tr> | ||
| − | <tr class="s2"><td class="l1">[[SADI|SADI Semantic | + | <tr class="s2"><td class="l1">CSS</td></tr> |
| − | <tr class=" | + | <tr class="s1"><td class="l1">[[SADI|SADI and SHARE <small>- a Semantic Web Service framework</small>]]</td></tr> |
| + | <tr class="s2"><td class="l1">[[CGI]]</td></tr> | ||
| + | <tr><td class="sp"> </td></tr> | ||
</table> | </table> | ||
| − | |||
===Statistics=== | ===Statistics=== | ||
| − | <table width=" | + | <table width="100%" > |
<tr class="s1"><td class="l1">[[Pattern discovery]]</td></tr> | <tr class="s1"><td class="l1">[[Pattern discovery]]</td></tr> | ||
<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="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 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="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="s2"><td class="l1">Cluster metrics <!-- (Cluster | + | <tr class="s2"><td class="l1">Cluster quality metrics <!-- (Cluster metrics (Akaike, BIC)–when and how) --></td></tr> |
<tr class="s1"><td class="l1">[[Map equation|The Map Equation]] </td></tr> | <tr class="s1"><td class="l1">[[Map equation|The Map Equation]] </td></tr> | ||
| − | <tr class="s2"><td class="l1">Machine learning < | + | <tr class="s2"><td class="l1">[[BIO Machine learning|Machine learning]]</td></tr> |
| − | <tr class="s1"><td class=" | + | <tr class="s1"><td class="l1">[[Information theory]]</td></tr> |
| − | <tr class="s2"><td class="l2">R plotting</td></tr> | + | |
| − | <tr class="s1"><td class="l2">[[R programming]]</td></tr> | + | <tr class="s2"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[R]] |
| − | <tr class="s2"><td class="l2">R EDA</td></tr> | + | <div class="mw-collapsible-content"> |
| − | <tr class="s1"><td class="l2">R regression</td></tr> | + | <table width="100%"><tr class="s1"><td class="l2">[[R tutorial|Introductory tutorial to '''R''']]</td></tr></table> |
| − | <tr class="s2"><td class="l2">R PCA</td></tr> | + | <table width="100%"><tr class="s2"><td class="l2">[[R plotting]]</td></tr></table> |
| − | <tr class="s1"><td class="l2">R Clustering</td></tr> | + | <table width="100%"><tr class="s1"><td class="l2">[[R programming]]</td></tr></table> |
| − | <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> | + | <table width="100%"><tr class="s2"><td class="l2">R EDA</td></tr></table> |
| − | <tr class=" | + | <table width="100%"><tr class="s1"><td class="l2">R regression</td></tr></table> |
| − | <tr class="s2"><td class="l2">[[ | + | <table width="100%"><tr class="s2"><td class="l2">R PCA</td></tr></table> |
| + | <table width="100%"><tr class="s1"><td class="l2">R Clustering</td></tr></table> | ||
| + | <table width="100%"><tr class="s2"><td class="l2">[[R Gene expression clustering]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s1"><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></table> | ||
| + | <table width="100%"><tr class="s2"><td class="l2">R hypothesis testing</td></tr></table> | ||
| + | <table width="100%"><tr class="s1"><td class="l2">[[Bioconductor]]</td></tr></table> | ||
| + | <table width="100%"><tr class="s2"><td class="l2">[[Regular Expressions]]</td></tr></table> | ||
| + | </div> | ||
| + | <tr class="s1"><td class="l1">Bayesian inference</td></tr> | ||
| + | |||
| + | <tr><td class="sp"> </td></tr> | ||
</table> | </table> | ||
===Applications=== | ===Applications=== | ||
| − | <table width=" | + | <table width="100%" > |
| − | <tr class="s1"><td class="l1">[[Data integration]] <!-- Add BioMart: Biodata integration, and data-mining of complex, related, descriptive data --></td></tr> | + | <tr class="s1"><td class="l1">[[BLAST scripting]]</td></tr> |
| + | <tr class="s2"><td class="l1">[[Chimera programming]]</td></tr> | ||
| + | <tr class="s1"><td class="l1">[[Data integration|Biological data access and 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="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="s1"><td class="l1">[[HMMER]]</td></tr> | ||
| − | <tr class="s2"><td class="l1">High-throughput sequencing</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="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> | + | <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) Expand to RNAseq--></td></tr> |
| + | <tr><td class="sp"> </td></tr> | ||
</table> | </table> | ||
</td></tr></table> | </td></tr></table> | ||
| − | |||
| Line 139: | Line 195: | ||
{{#lst:Computational_Systems_Biology_Main_Page|CSB_main_grading}} | {{#lst:Computational_Systems_Biology_Main_Page|CSB_main_grading}} | ||
| − | + | --> | |
== Resources == | == Resources == | ||
;Course related | ;Course related | ||
| Line 146: | Line 202: | ||
;Contents related | ;Contents related | ||
| − | * | + | *'''[[UCSF_Chimera|Chimera]]''' |
*A '''[[Stereo Vision]]''' tutorial | *A '''[[Stereo Vision]]''' tutorial | ||
| + | *[[Workshops]] taught elsewhere | ||
| − | + | <!-- | |
<table width="100%" padding="10" border="1"> | <table width="100%" padding="10" border="1"> | ||
<tr> | <tr> | ||
Latest revision as of 16:38, 1 May 2017
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
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
Resources
- Course related
- Netiquette for the Group mailing list
- Contents related
- Chimera
- A Stereo Vision tutorial
- Workshops taught elsewhere
