Difference between revisions of "Applied Bioinformatics Main Page"
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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}} | |
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| + | <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> | ||
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| − | + | {{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> | ||
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===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 177: | 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> | ||
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{{#lst:Computational_Systems_Biology_Main_Page|CSB_main_grading}} | {{#lst:Computational_Systems_Biology_Main_Page|CSB_main_grading}} | ||
| − | + | --> | |
== Resources == | == Resources == | ||
;Course related | ;Course related | ||
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;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
