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teaching.html
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<!DOCTYPE html>
<html class="html">
<head>
<meta http-equiv="Content-type" content="text/html;charset=UTF-8"/>
<meta name="generator" content="7.3.5.244"/>
<title>Teaching</title>
<!-- CSS -->
<link rel="stylesheet" type="text/css" href="css/site_global.css?3983832653"/>
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<a class="nonblock nontext MenuItem MenuItemWithSubMenu clearfix colelem" id="u1006" href="index.html"><!-- horizontal box --><div class="MenuItemLabel NoWrap clearfix grpelem" id="u1008-4"><!-- content --><p>Home</p></div></a>
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<a class="nonblock nontext MenuItem MenuItemWithSubMenu clearfix colelem" id="u949" href="research.html"><!-- horizontal box --><div class="MenuItemLabel NoWrap clearfix grpelem" id="u952-4"><!-- content --><p>Research</p></div></a>
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<a class="nonblock nontext MenuItem MenuItemWithSubMenu clearfix colelem" id="u933" href="programming.html"><!-- horizontal box --><div class="MenuItemLabel NoWrap clearfix grpelem" id="u936-4"><!-- content --><p>Programming</p></div></a>
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<div class="rgba-background clearfix colelem" id="u431-6"><!-- content -->
<p id="u431"> </p>
<p id="u431-3">I have been lucky to teach in workshops on Bioinformatics. Here are some presentations I have used in the past. Feel free to use and modify them.</p>
<p> </p>
</div>
<div class="PamphletWidget clearfix colelem" id="pamphletu1193"><!-- none box -->
<div class="popup_anchor" id="u1205popup">
<div class="ContainerGroup clearfix" id="u1205"><!-- stack box -->
<div class="Container clearfix grpelem" id="u1206"><!-- group -->
<div class="clearfix grpelem" id="u1207-17"><!-- content -->
<p id="u1207-3"><span><span class="actAsDiv normal_text" id="u1208"><!-- content --><span class="actAsDiv clip_frame" id="u1209"><!-- image --></span></span></span><span id="u1207-2">Measuring microbial</span></p>
<p id="u1207-5">Diversity</p>
<p id="u1207-6"> </p>
<p id="u1207-8">Microbes mediate many globally important processes such as carbon and nitrogen cycle. So it is important to understand how microbial communities work. The study of microbial communities include the characterization of the members of the community in terms of novelty, the structuring of the microbial community and the relationship among communities within and between ecosystems.</p>
<p id="u1207-10">This presentation covers basic topics of alpha and beta diversity and analysis of microbial diversity using 16S rRNA gene sequencing.</p>
<p id="u1207-11"> </p>
<p id="u1207-15">Get the Presentation <a class="nonblock" href="assets/1.-measuring-microbial-diversity.pptx">here.</a></p>
</div>
<div class="clip_frame grpelem" id="u1382"><!-- image -->
<img class="block" id="u1382_img" src="images/picture1.jpg" alt="" width="133" height="126"/>
</div>
</div>
<div class="Container invi clearfix grpelem" id="u1211"><!-- group -->
<div class="clip_frame grpelem" id="u1376"><!-- image --></div>
<div class="clearfix grpelem" id="u1212-16"><!-- content -->
<p id="u1212-3"><span><span class="actAsDiv normal_text" id="u1213"><!-- content --><span class="actAsDiv clip_frame" id="u1214"><!-- image --></span></span></span><span>Tools for microbial community analysis</span></p>
<p id="u1212-4"> </p>
<p id="u1212-6"><span>This presentation covers the rationale behind multiple techniques for microbial community analysis including clone libraries , pyrosequencing, T-RFLP, DGGE, phylogenetic arrays, fingerprinting and sequencing.</span></p>
<p id="u1212-7"> </p>
<p id="u1212-9"><span>Some of the techniques are outdated by next-generation sequencing though they are still inexpensive and informative to some extent.</span></p>
<p id="u1212-10"> </p>
<p id="u1212-14">Get the Presentation<a class="nonblock" href="assets/2.-tools-for-microbial-community-analysis-.pptx"> here.</a></p>
</div>
<div class="clip_frame grpelem" id="u1421"><!-- image -->
<img class="block" id="u1421_img" src="images/picture3.jpg" alt="" width="156" height="238"/>
</div>
</div>
<div class="Container invi clearfix grpelem" id="u1216"><!-- group -->
<div class="clearfix grpelem" id="u1217-13"><!-- content -->
<p id="u1217-3"><span><span class="actAsDiv normal_text" id="u1218"><!-- content --><span class="actAsDiv clip_frame" id="u1219"><!-- image --></span></span></span>Alignments and phylogenetic trees</p>
<p id="u1217-4"> </p>
<p id="u1217-6">Trees are tools to represent the evolutionary story of sequences. Alignment is the first and most critical step for comparison of sequences. In this presentation the rationale and algorithms behind alignment and phylogenetic tree reconstruction including distance- and character-based algorithms.</p>
<p id="u1217-7"> </p>
<p id="u1217-11">Get the Presentation <a class="nonblock" href="assets/3.-alignments-and-phylogenetic-trees.pptx">here.</a></p>
</div>
<div class="clip_frame grpelem" id="u1426"><!-- image -->
<img class="block" id="u1426_img" src="images/picture4.jpg" alt="" width="146" height="126"/>
</div>
</div>
<div class="Container invi clearfix grpelem" id="u1255"><!-- group -->
<div class="clearfix grpelem" id="u1337-19"><!-- content -->
<p id="u1337-3"><span><span class="actAsDiv normal_text" id="u1338"><!-- content --><span class="actAsDiv clip_frame" id="u1339"><!-- image --></span></span></span>Ribosomal Databases</p>
<p id="u1337-4"> </p>
<p id="u1337-9">Ribosomal rNA gene databases are powerful tools for the study of microbial communities because they provide specialized tools as well as organized and curated data. This presentation shows the different analysis tools of the <a class="nonblock" href="http://rdp.cme.msu.edu/">Ribosomal Database Project</a> . One of the most popular rRNA gene Database and my favorite one (I worked there for a while).</p>
<p id="u1337-13">Get the presentation<a class="nonblock" href="assets/4.ribosomal-rna-databases.pptx"> here.</a></p>
<p id="u1337-16"><a class="nonblock" href="http://rna.ucsc.edu/rnacenter/ribosome_images.html">Image credit</a></p>
<p id="u1337-17"> </p>
</div>
<div class="clip_frame grpelem" id="u1431"><!-- image -->
<img class="block" id="u1431_img" src="images/ecoli_16s.jpg" alt="" width="186" height="236"/>
</div>
</div>
<div class="Container invi clearfix grpelem" id="u1263"><!-- group -->
<div class="clearfix grpelem" id="u1342-20"><!-- content -->
<p id="u1342-3"><span><span class="actAsDiv normal_text" id="u1343"><!-- content --><span class="actAsDiv clip_frame" id="u1344"><!-- image --></span></span></span><span>RDP Pyrosequencing pipeline</span></p>
<p id="u1342-4"> </p>
<p id="u1342-6">This presentation covers the basic processing of 16S rRNA sequences from pyrosequencing using the Ribosomal database Project.</p>
<p id="u1342-14">The RDP pipeline is located<a class="nonblock" href="http://pyro.cme.msu.edu/"> here.</a>. Image from <a class="nonblock" href="http://rdp.cme.msu.edu/">RDP</a>.</p>
<p id="u1342-18">Get the presentation <a class="nonblock" href="assets/5.rdp-pipeline-pyrosequencing-pipeline.pptx">here.</a></p>
</div>
<div class="clip_frame grpelem" id="u1436"><!-- image -->
<img class="block" id="u1436_img" src="images/picture1.gif" alt="" width="189" height="151"/>
</div>
</div>
<div class="Container invi clearfix grpelem" id="u1265"><!-- group -->
<div class="clearfix grpelem" id="u1347-12"><!-- content -->
<p id="u1347-3"><span><span class="actAsDiv normal_text" id="u1348"><!-- content --><span class="actAsDiv clip_frame" id="u1349"><!-- image --></span></span></span>BLAST</p>
<p id="u1347-4"> </p>
<p id="u1347-6">The basic local alignment search tools (BLAST) is one of the most widely used bioinformatic tools in science. In this presentattion the basic algorithm , the statistics, and the different flavors of BLAST are explained. Also is explained how to run BLAST locally and on the web.</p>
<p id="u1347-10">Get the presentation <a class="nonblock" href="assets/6.blast.pptx">here.</a></p>
</div>
<div class="clip_frame grpelem" id="u1441"><!-- image -->
<img class="block" id="u1441_img" src="images/200px-us-nlm-ncbi-logosvg.jpg" alt="" width="137" height="169"/>
</div>
</div>
<div class="Container invi clearfix grpelem" id="u1267"><!-- group -->
<div class="clearfix grpelem" id="u1352-16"><!-- content -->
<p id="u1352-3"><span><span class="actAsDiv normal_text" id="u1353"><!-- content --><span class="actAsDiv clip_frame" id="u1354"><!-- image --></span></span></span>Functional gene repository and pipeline</p>
<p id="u1352-4"> </p>
<p id="u1352-9">This presentation covers the features of the <a class="nonblock" href="http://fungene.cme.msu.edu/">RDP Functional gene Pipeline and repository</a>. Here the basics of Hidden Markov models and the processing of pyrosequencing data of functional genes using the webtools are explained .</p>
<p id="u1352-13">Get the presentation <a class="nonblock" href="assets/7.functional-gene-repository-and-pipeline.pptx">here.</a></p>
<p id="u1352-14"> </p>
</div>
<div class="clip_frame grpelem" id="u1456"><!-- image --></div>
<div class="clip_frame grpelem" id="u1461"><!-- image -->
<img class="block" id="u1461_img" src="images/picture2.jpg" alt="" width="196" height="209"/>
</div>
</div>
<div class="Container invi clearfix grpelem" id="u1269"><!-- group -->
<div class="clearfix grpelem" id="u1357-13"><!-- content -->
<p id="u1357-3"><span><span class="actAsDiv normal_text" id="u1358"><!-- content --><span class="actAsDiv clip_frame" id="u1359"><!-- image --></span></span></span>Bioinformatic databases</p>
<p id="u1357-4"> </p>
<p id="u1357-6">This presentation covers the most commonly used bioinformatics databases</p>
<p id="u1357-7"> </p>
<p id="u1357-11">Get the presentation <a class="nonblock" href="assets/8.-databases.pptx">here.</a></p>
</div>
<div class="clip_frame grpelem" id="u1468"><!-- image -->
<img class="block" id="u1468_img" src="images/picture32.jpg" alt="" width="143" height="134"/>
</div>
</div>
</div>
</div>
<div class="ThumbGroup clearfix grpelem" id="u1198"><!-- none box -->
<div class="popup_anchor">
<div class="Thumb popup_element rgba-background clearfix" id="u1203"><!-- group -->
<div class="clearfix grpelem" id="u1204-4"><!-- content -->
<p>Measuring microbial diversity</p>
</div>
</div>
</div>
<div class="popup_anchor">
<div class="Thumb popup_element rgba-background clearfix" id="u1201"><!-- group -->
<div class="clearfix grpelem" id="u1202-4"><!-- content -->
<p>Tools for microbial community analysis</p>
</div>
</div>
</div>
<div class="popup_anchor">
<div class="Thumb popup_element rgba-background clearfix" id="u1199"><!-- group -->
<div class="clearfix grpelem" id="u1200-4"><!-- content -->
<p>Alignments and phylogenetic trees</p>
</div>
</div>
</div>
<div class="popup_anchor">
<div class="Thumb popup_element rgba-background clearfix" id="u1261"><!-- group -->
<div class="clearfix grpelem" id="u1271-4"><!-- content -->
<p>Ribosomal RNA databases</p>
</div>
</div>
</div>
<div class="popup_anchor">
<div class="Thumb popup_element rgba-background clearfix" id="u1264"><!-- group -->
<div class="clearfix grpelem" id="u1272-3"><!-- content -->
<p> </p>
</div>
<div class="clearfix grpelem" id="u1279-4"><!-- content -->
<p>RDP pyrosequencing pipeline</p>
</div>
</div>
</div>
<div class="popup_anchor">
<div class="Thumb popup_element rgba-background clearfix" id="u1266"><!-- group -->
<div class="clearfix grpelem" id="u1278-4"><!-- content -->
<p>BLAST</p>
</div>
</div>
</div>
<div class="popup_anchor">
<div class="Thumb popup_element rgba-background clearfix" id="u1268"><!-- group -->
<div class="clearfix grpelem" id="u1277-4"><!-- content -->
<p>Functional gene repository and pipeline</p>
</div>
</div>
</div>
<div class="popup_anchor">
<div class="Thumb popup_element rgba-background clearfix" id="u1270"><!-- group -->
<div class="clearfix grpelem" id="u1276-4"><!-- content -->
<p>Other databases</p>
</div>
</div>
</div>
</div>
</div>
<div class="clearfix colelem" id="u1245-3"><!-- content -->
<p> </p>
</div>
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