Curriculum for 2018 Computational Immunology Summer School

Introduction to Computational Biology with Dr. Kepler

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(‘devtools’)
  • install.packages(‘tidyverse’)

Install the GitHub pakcage

  • devtools::install_github(“wesm/feather/R”)

Install BioConductor packages

  • source(“”)
  • biocLite(“cytofkit”)
  • biocLite(“flowCore”)
  • biocLite(“flowiz”)
  • biocLite(“flowMeans”)

Students can clone my repository.

Antibody Structure with Dr. Moretti
This review article will form the core of the talk. We will use the Chimera software package, which has this tutorial for new users. If you are already familiar with PyMol you can use this alternative software package.

PDF documents from Dr. Moretti’s presentation are available: slides and tutorial

Single-cell RNA-seq with Dr. Johnson
Here is the software you will need installed on your machines beforehand to participate in the hands on tutorial:
R (version 3.5 or greater)
Bioconductor version 3.7. From the R console type the following:
> source(‘’)
> biocLite()
Johnson Lab Single Cell Toolkit. From the R console type the following:
> biocLite(‘singleCellTK’)
Rsubread for sequencing read alignment. From the R console type the following:
> biocLite(‘Rsubread’)
This software only works on linux and Mac OS, but is only a small part of the tutorial.
No documents are needed, but I will  provide some papers as references. It is best to refer to these after the course.

Link for Dr. Johnson’s class


Molecular Evolution with Dr. Matsen
Course Outline
seaview software package

B-Cell Clonal Analysis Dr. Kepler

How to set up and connect to an Azure virtual machine. Step-by-step procedure: Azure VM establishment

AVA data
Cloanalyst Installer

Please find the zip archive called at the dropbox folder to which you have been invited.

Dynamical Modeling with Dr. Zarnitsnya
I will be using the models from the attached paper  to illustrate the process of developing and using systems of ODEs in solving scientific problems. Reading the paper before the class is optional. Students will need to have R and RStudio installed. I will be using some apps from the package Dynamical Systems Approach to Immune Response Modeling DSAIRM. There are instructions on how to install the DSAIRM package on that site, and it should be easy to do so.

R code for the models we discussed.

Here is a copy of the slides from my presentation.