MPGI Workshop: Intro to MSI (Module 1)

This is Module 1 of a 4 part tutorial series.  
To register for Module 2, Intro to Genomics Terminology and Analyses, click here
To register for Module 3, Intro to PBS Scripts and Job Queues, click here
To regsiter for Module 4, Job Parallelization with Task Arrays and GNU Parallel, click here

Introduction to Deep Learning with Caffe and Tensorflow

Deep Learning has emerged as an important new tool for a range of research applications. Emerging programs such as Caffe and Tensorflow are available at MSI and can be executed on Nvidia GPU resources. In this tutorial, MSI and Nvidia instructors will walk through an interactive exercise running some of these programs. Participants will be able to login to a node with a GPU to work through introductory exercises. We will also show how to run these programs in batch jobs on MSI systems.


Getting started with XSEDE resources

The NSF has a number of computational resources available to University staff and students as part of the XSEDE program. These computers have a lot in common with MSI systems, but there are a few important differences. This hands-on tutorial will introduce MSI researchers to multiple XSEDE resources. Participants will receive access to the Stampede 2 and Jetstream systems to run example jobs. This tutorial will cover the basics of policies, data movement, submitting jobs, and connecting to machines that are part of XSEDE.

Interacting with dbGaP data on Stratus

MSI has deployed a cloud service for research computing called Stratus. In its initial iteration, Stratus is designed expressly to satisfy the requirements set forth by the NIH Genomic Data Sharing (GDS) Policy for data from the Database of Genotypes and Phenotypes (i.e., dbGaP data). This tutorial introduces Stratus to users who wish to process dbGaP data at MSI, and gives them an interactive lesson on how to access the service, deploy their first virtual machines, and move data through multiple tiers of storage. 

Quality Control of Illumina Data at the Command Line

Want to take your analysis to the next level? 

This hands-on tutorial will introduce new bioinformaticitions to the skills needed to start to build more complex analysis pipelines. This tutorial will take you though the steps needed to run standard quality control analysis on Illumina data using scripting to automate the analysis. 

In this tutorial you will be introduced to: