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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"> | ||
| + | Continue [[BCB410|'''here''']] for the current BCB410H course page ... | ||
| + | </div> | ||
| + | |||
| + | {{Vspace}} | ||
<div class="alert"> | <div class="alert"> | ||
| − | Continue [[ | + | Continue [[BCB330|'''here''']] for guidelines on BCB330Y and BCB430Y projects with me ... |
</div> | </div> | ||
| − | |||
| − | + | {{Vspace}} | |
==Topics== | ==Topics== | ||
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===Programming=== | ===Programming=== | ||
<table width="100%" > | <table width="100%" > | ||
| − | <tr class=" | + | <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> | ||
| Line 90: | Line 94: | ||
<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> | ||
| Line 100: | Line 104: | ||
===Algorithms=== | ===Algorithms=== | ||
<table width="100%" > | <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 123: | 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=== | ||
| Line 143: | Line 151: | ||
<tr class="s2"><td class="l1">Cluster quality metrics <!-- (Cluster metrics (Akaike, BIC)–when and how) --></td></tr> | <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]]</td></tr> | + | <tr class="s2"><td class="l1">[[BIO Machine learning|Machine learning]]</td></tr> |
<tr class="s1"><td class="l1">[[Information theory]]</td></tr> | <tr class="s1"><td class="l1">[[Information theory]]</td></tr> | ||
| Line 155: | Line 163: | ||
<table width="100%"><tr class="s2"><td class="l2">R PCA</td></tr></table> | <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="s1"><td class="l2">R Clustering</td></tr></table> | ||
| − | <table width="100%"><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> | + | <table width="100%"><tr class="s2"><td class="l2">[[R Gene expression clustering]]</td></tr></table> |
| − | <table width="100%"><tr class=" | + | <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=" | + | <table width="100%"><tr class="s2"><td class="l2">R hypothesis testing</td></tr></table> |
| − | <table width="100%"><tr class=" | + | <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> | </div> | ||
<tr class="s1"><td class="l1">Bayesian inference</td></tr> | <tr class="s1"><td class="l1">Bayesian inference</td></tr> | ||
| Line 167: | Line 176: | ||
===Applications=== | ===Applications=== | ||
<table width="100%" > | <table width="100%" > | ||
| + | <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="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> | ||
| Line 172: | Line 183: | ||
<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> | <tr><td class="sp"> </td></tr> | ||
</table> | </table> | ||
| Line 184: | 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 191: | 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
