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:

Basics of RNA-Seq Data Analysis - Lecture

This lecture will cover the basics of RNA-Seq experimental design and data quality assessment, followed by an overview of data analysis for the detection of differentally expressed genes.  Specific subtopics include:

Analysis of PacBio Sequencing Data Using SMRT Portal

This hands-on tutorial will cover installation and use of the SMRT portal at MSI to analyze PacBio sequencing data. The basics of full genome assembly and transcript assembly will be covered.  At the end of this tutorial, participants should be able to:

PacBio Sequencing - Lecture

This lecture will cover the special capabilities and use cases of PacBio sequencing as well as the basics of data analysis. Specific subtopics include:

  • Technology overview (physical basis of sequencing, pros and cons compared with other sequencing technologies)
  • De novo assembly applications (N50 and other assembly concepts, HGAP algorithm, diploid assembly)
  • IsoSeq transcriptome assessment (motivation, experimental procedure, biological applications, analysis approaches)
  • Visualization of PacBio data with new IGV features

Data Storage Systems and Data Analysis Workflows for Research

In this tutorial you will learn about the data storage systems available for academic research at the University of Minnesota. An overview of the kinds of storage systems that are available, policies for getting access to them, a comparison of their characteristics, and examples of how they can be accessed will be presented. You will also be given an overview of how the characteristics of UMN storage will impact the stability and throughput of various applications and workflows.


This one-day, hands-on workshop provides an introduction on how to write a parallel program using MPI and will help researchers write better and portable parallel codes for distributed-memory Linux clusters. The tutorial will focus on basic point-to-point communication and collective communications, which are the most commonly used MPI routines in high- performance scientific computation. In addition, the advantage of using MPI non-blocking communication will be introduced. Each session of the workshop will combine a lecture with hands-on practice.


Intended Audience

Undergraduate and graduate students with some familiarity with finite element method, plus faculty interested in finite element analysis, optimization, or fatigue.

The SIMULIA Central’s Minneapolis office invites you to two-part seminar held on campus to provide an introductory, hands-on workshop with Abaqus and to introduce you to additional simulation technology recently made available to the University of Minnesota.


Compiling and Debugging

This tutorial will help users learn the basics of compiling and debugging their code on MSI systems. Particular attention will be paid to code written in Fortran, C, and C++. Basic methods for debugging will be outlined, with users being able to explore different debugging tools. This tutorial will focus primarily on compiling serial programs,but brief information on compiling and debugging parallel programs will also be given. Attendees should have a basic knowledge of Linux and rudimentary knowledge of a programming language.

Interactive Computing

This two part tutorial will first introduce you to the concept of interactive high performance computing, as distinct from batch computing. We will cover the Citrix (Windows) and NICE EnginFrame (Linux) interactive computing environments hosted by MSI. Attendees will learn how to launch virtual desktops at MSI, connect to a variety of resources, load software modules, and build complex research workflows.