{"id":1486,"date":"2018-06-06T15:26:16","date_gmt":"2018-06-06T19:26:16","guid":{"rendered":"https:\/\/www.bu.edu\/computationalimmunology\/?page_id=1486"},"modified":"2018-06-19T11:46:09","modified_gmt":"2018-06-19T15:46:09","slug":"curriculum-for-2018-computational-immunology-summer-school","status":"publish","type":"page","link":"https:\/\/www.bu.edu\/computationalimmunology\/summer-schools-and-symposia\/curriculum-for-2018-computational-immunology-summer-school\/","title":{"rendered":"Curriculum for 2018 Computational Immunology Summer School"},"content":{"rendered":"<p><strong>Introduction to Computational Biology <\/strong>with Dr. Kepler<\/p>\n<p><a target=\"_blank\" href=\"\/computationalimmunology\/files\/2018\/06\/TBK1.zip\">Introduction<\/a><br \/>\n<a href=\"\/computationalimmunology\/files\/2018\/06\/Lecture-1.pdf\">Lecture 1<\/a><\/p>\n<p><strong>Computational Analysis of Cytometric Data I and II<\/strong> with Drs. Belkina and Chan<br \/>\nWe will use <a target=\"_blank\" href=\"https:\/\/www.anaconda.com\/download\">Anaconda Python<\/a> and <a target=\"_blank\" href=\"https:\/\/github.com\/IRkernel\/Irkernel \">R Kernel for Jupyter<\/a>.<\/p>\n<p><strong><em>Tuesday morning session <\/em><\/strong><em>with Dr. Chan<\/em><br \/>\n<em>Install the following CRAN packages<\/em><\/p>\n<ul>\n<li>install.packages(&#8216;devtools&#8217;)<\/li>\n<li>install.packages(&#8216;tidyverse&#8217;)<\/li>\n<\/ul>\n<p><em>Install the GitHub pakcage<\/em><\/p>\n<ul>\n<li>devtools::install_github(&#8220;wesm\/feather\/R&#8221;)<\/li>\n<\/ul>\n<p><em>Install BioConductor packages<\/em><\/p>\n<ul>\n<li>source(&#8220;https:\/\/bioconductor.org\/biocLite.R&#8221;)<\/li>\n<li>biocLite(&#8220;cytofkit&#8221;)<\/li>\n<li>biocLite(&#8220;flowCore&#8221;)<\/li>\n<li>biocLite(&#8220;flowiz&#8221;)<\/li>\n<li>biocLite(&#8220;flowMeans&#8221;)<\/li>\n<\/ul>\n<p>Students can clone my <a href=\"https:\/\/github.com\/cliburn\/boston_computational_immunology.git\" rel=\"noopener\" target=\"_blank\">repository.<\/a><\/p>\n<p><strong>Antibody Structure<\/strong>\u00a0with Dr. Moretti<br \/>\nThis <a target=\"_blank\" href=\"\/computationalimmunology\/files\/2018\/06\/Moretti-review-article-AID-0024-2014.pdf\"> review article<\/a> will form the core of the talk. We will use the <a target=\"_blank\" href=\"https:\/\/www.cgl.ucsf.edu\/chimera\/\"> Chimera<\/a> software package, which has this <a target=\"_blank\" href=\"https:\/\/www.cgl.ucsf.edu\/chimera\/docs\/UsersGuide\/frametut.html\"> tutorial <\/a>for new users. If you are already familiar with PyMol you can use this <a target=\"_blank\" href=\"https:\/\/pymol.org\/\"> alternative <\/a> software package.<\/p>\n<p>PDF documents from Dr. Moretti&#8217;s presentation are available:\u00a0<a href=\"\/computationalimmunology\/files\/2018\/06\/AntibodyStructure2018SummerSchool.pdf\" target=\"_blank\">slides<\/a>\u00a0and\u00a0<a href=\"\/computationalimmunology\/files\/2018\/06\/AntibodyStructure2018SummerSchool_tutorial.pdf\" target=\"_blank\">tutorial<\/a><\/p>\n<p><strong>Single-cell RNA-seq<\/strong> with Dr. Johnson<br \/>\nHere is the software you will need installed on your machines beforehand to participate in the hands on tutorial:<br \/>\n<a target=\"_blank\" href=\"http:\/\/archive.linux.duke.edu\/cran\/\">R <\/a> (version 3.5 or greater)<br \/>\n<a target=\"_blank\" href=\"https:\/\/www.rstudio.com\/products\/rstudio\/download\/#download \">RStudio <\/a><br \/>\n<a target=\"_blank\" href=\"https:\/\/bioconductor.org\/biocLite.R\"> Bioconductor <\/a> version 3.7. From the R console type the following:<br \/>\n&gt; source(&#8216;https:\/\/bioconductor.org\/biocLite.R&#8217;)<br \/>\n&gt; biocLite()<br \/>\nJohnson Lab Single Cell Toolkit. From the R console type the following:<br \/>\n&gt; biocLite(&#8216;singleCellTK&#8217;)<br \/>\nRsubread for sequencing read alignment. From the R console type the following:<br \/>\n&gt; biocLite(\u2018Rsubread&#8217;)<br \/>\nThis software only works on linux and Mac OS, but is only a small part of the tutorial.<br \/>\nNo documents\u00a0are needed, but I will\u00a0\u00a0provide some papers as references. It is best to refer to these after the course.<\/p>\n<p><span style=\"color: #000000;\">L<\/span>ink\u00a0for Dr. Johnson&#8217;s class<\/p>\n<p>&nbsp;<\/p>\n<p><strong>Molecular Evolution\u00a0<\/strong>with<strong>\u00a0<\/strong>Dr. Matsen<br \/>\n<a target=\"_blank\" href=\"https:\/\/matsen.github.io\/teaching\/courses\/bu-summer-school\/\"> Course Outline<\/a><br \/>\n<a target=\"_blank\" href=\"http:\/\/doua.prabi.fr\/software\/seaview \"> seaview<\/a>\u00a0software package<\/p>\n<p><strong>B-Cell Clonal Analysis<\/strong> Dr. Kepler<\/p>\n<p>How to set up and connect to an Azure virtual machine. Step-by-step procedure: <a href=\"\/computationalimmunology\/files\/2018\/06\/Azure-VM-establishment.pdf\">Azure VM establishment<\/a><\/p>\n<p><a href=\"\/computationalimmunology\/files\/2018\/06\/AVA-S5-data.zip\" target=\"_blank\">AVA data<\/a><br \/>\n<a href=\"\/computationalimmunology\/files\/2018\/06\/Cloanalyst.zip\" target=\"_blank\">Cloanalyst Installer<\/a><\/p>\n<p>Please find the zip archive called ARPAssembler.zip at the dropbox folder to which you have been invited.<\/p>\n<p><strong>Dynamical Modeling<\/strong>\u00a0with Dr. Zarnitsnya<br \/>\nI will be using the models from the <a target=\"_blank\" href=\"\/computationalimmunology\/files\/2018\/06\/Zarnitsyna16pp.pdf\"> attached paper\u00a0<\/a> to illustrate the\u00a0process of developing and using systems of\u00a0ODEs\u00a0in solving\u00a0scientific problems. Reading the paper before the class\u00a0is optional. Students will need to have <a target=\"_blank\" href=\"http:\/\/archive.linux.duke.edu\/cran\/\">R<\/a> and <a target=\"_blank\" href=\"https:\/\/www.rstudio.com\/products\/rstudio\/download\/#download \"> RStudio <\/a> installed. I will be using some apps from the package Dynamical Systems Approach to Immune Response Modeling <a target=\"_blank\" href=\"https:\/\/github.com\/ahgroup\/DSAIRM\"> DSAIRM<\/a>. There are instructions on how to install the DSAIRM package on that site, and it should be easy to do so.<\/p>\n<p><a href=\"\/computationalimmunology\/files\/2018\/06\/DynamicalModelsVeronikaZarnitsyna.zip\" target=\"_blank\">R code<\/a>\u00a0for the models we discussed.<\/p>\n<p>Here is a copy of the <a href=\"\/computationalimmunology\/files\/2018\/06\/U19SummerSchool2018VZ.pdf\" rel=\"noopener\" target=\"_blank\">slides<\/a> from my presentation.<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Introduction to Computational Biology with Dr. Kepler Introduction Lecture 1 Computational Analysis of Cytometric Data I and II with Drs. Belkina and Chan We will use Anaconda Python and R Kernel for Jupyter. Tuesday morning session with Dr. Chan Install the following CRAN packages install.packages(&#8216;devtools&#8217;) install.packages(&#8216;tidyverse&#8217;) Install the GitHub pakcage devtools::install_github(&#8220;wesm\/feather\/R&#8221;) Install BioConductor packages source(&#8220;https:\/\/bioconductor.org\/biocLite.R&#8221;) [&hellip;]<\/p>\n","protected":false},"author":8058,"featured_media":0,"parent":948,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www.bu.edu\/computationalimmunology\/wp-json\/wp\/v2\/pages\/1486"}],"collection":[{"href":"https:\/\/www.bu.edu\/computationalimmunology\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bu.edu\/computationalimmunology\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bu.edu\/computationalimmunology\/wp-json\/wp\/v2\/users\/8058"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bu.edu\/computationalimmunology\/wp-json\/wp\/v2\/comments?post=1486"}],"version-history":[{"count":50,"href":"https:\/\/www.bu.edu\/computationalimmunology\/wp-json\/wp\/v2\/pages\/1486\/revisions"}],"predecessor-version":[{"id":1613,"href":"https:\/\/www.bu.edu\/computationalimmunology\/wp-json\/wp\/v2\/pages\/1486\/revisions\/1613"}],"up":[{"embeddable":true,"href":"https:\/\/www.bu.edu\/computationalimmunology\/wp-json\/wp\/v2\/pages\/948"}],"wp:attachment":[{"href":"https:\/\/www.bu.edu\/computationalimmunology\/wp-json\/wp\/v2\/media?parent=1486"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}