All Tutorials

  • Thu Oct 3, 1:00 pm - 4:00 pm
    Walter Library

    This is a practical, hands-on tutorial designed to give participants experience analyzing next-generation sequence (NGS) data in Galaxy. Attendees will learn how to access their UMGC sequence datasets in Galaxy using Data Libraries, how to evaluate sequence quality using FastQC, and how to correct quality issues using trimming and filtering tools. These are the initial steps required for any NGS experiment, including RNA-Seq analysis or variant discovery. Attendees will also learn about data sharing and workflow building in Galaxy.

  • Mon Sep 30, 9:00 am - 4:00 pm
    Walter Library

    Invited Speaker: Matthew G. Knepley, University of Chicago

    Dr. Knepley is an author of the widely used PETSc library for scientific computing from ANL, and is a principal designer of the PyLith library for the solution of dynamic and quasi-static tectonic deformation problems.


    PETSc, is a suite of data structures and routines for the scalable parallel solution of scientific applications, often modeled by partial differential equations. It supports MPI, shared memory pthreads, and GPUs, as well as hybrid MPI-shared memory pthreads or MPI-GPU parallelism.

    In this tutorial, we will cover basic sparse parallel linear algebra, as well as linear and nonlinear algebraic solvers, and timestepping. Students will learn to use the dynamic configuration object system in PETSc, and use it to assemble hierarchical, multilevel solvers for multiphysics problems. We will also learn to debug and profile the resulting applications.

    The Morning session will cover Basic Usage:

    • Vectors and Matrices

    • Generic Solver Setup

    • Dynamic Object Configuration

    • Debugging and Profiling

    The Afternoon session will cover Advanced Usage:

    • Structured Meshes using DMDA

    • Linear Preconditioning

    • Structured Linear Multigrid

    • Block Preconditioners

    • Nonlinear Solvers

    • Nonlinear Preconditioners

    • Timestepping


    • Participants are invited to bring their own laptops to the tutorial

    • Participants should visit the PETSc Website,, and install PETSc. You can install the latest release, but the most up-to-date snapshot is preferred, which would use the 'git checkout next' branch and is available at the following link,

    • Detailed information on the speaker and related material can be found here:

  • Thu Sep 26, 10:00 am - 4:00 pm
    Walter Library

    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. The lecture will introduce basic principles, and the hands-on portion will focus on the use of MPI principles via examples.

    Session 1: Introduction to basic concepts of MPI, centering on point-to-point communication.

    Session 2: MPI collective communications including broadcast, gather, scatter, and All-to-All. Programming will be done in Fortran and C, so any background in these two languages will be helpful.

  • Tue Sep 24, 9:00 am - 11:00 am
    Walter Library

    This tutorial is designed to provide advanced information on RNA-seq analysis, including visualization tools, alternative analysis packages, other applications of RNA-seq, and trouble-shooting of common analysis problems. After this tutorial attendees will be able to analyze RNA-seq data independently or in collaboration with MSI.

    This tutorial discusses the broad impact of RNA-seq technology and outlines advanced tools to be used in the RNA-seq analysis pipeline with a focus on the visualization and effective presentation of the data and results. It also discusses “real world” issues in RNA-seq analysis, so that attendees will learn about the common errors and misunderstandings in the analysis and feel more comfortable running the analysis.

  • Wed Sep 18, 9:00 am - 11:00 am
    Walter Library

    This tutorial is designed to give experimental scientists a thorough overview of the practical issues involved in designing an RNA-seq experiment and the best practices in analysis of RNA-seq data. After this tutorial, attendees will be aware of the most important factors affecting the successful outcome of an RNA-seq experiment and understand the process for properly analyzing the data.

    This tutorial discusses the main parameters involved in experimental design including read length and depth, and replication required for robust statistical analysis, as well as the main steps of RNA-seq analysis: data quality assessment, data trimming and filtering, read mapping, transcriptome assembly and analysis, transcript abundance estimation, and differential expression analysis. Commonly used software and resources for addressing these steps will be discussed. Detailed instruction on using specific software packages will be provided in other tutorials.

  • Thu Sep 12, 1:00 pm - 3:00 pm
    Walter Library

    This tutorial is geared to new MSI users and will provide an introduction to the facilities and computational resources at MSI. The quick start portion of the tutorial will provide instructions for accessing these resources such as setting up accounts, submitting jobs on the various machines, etc. We will conclude with a brief introduction of the MSI Unix environment, including hands-on examples. The UNIX operating system is a fundamental part of the MSI experience for people using the MSI Linux workstations and core systems. Many of MSI’s scientific codes require that the user understand basic UNIX operating commands and functionality. This tutorial will give the novice user an introduction to using the UNIX operating environment to navigate around and use MSI resources.

  • Tue Aug 27, 1:00 pm - 3:00 pm
    Walter Library

    Kai Mollerud, CEMS, Dan McDonald, CEMS, Ravishankar Chityala, MSI, Shuxia Zhang, MSI

    Matlab currently is one of the most practical software used for numerical calculations. This tutorial will introduce the basic components of general purpose GPU (GPGPU) computing that can dramatically accelerate some Matlab applications. In addition to accessing the hardware resources (Cascade cluster, Koronis and GPUT nodes), we will discuss what type of applications can be run, how to execute the calculations on GPU device, and what kind of performance gains it can provide.

    A hands-on practice session will follow the lecture. Provided examples will enable the attendees to get direct experience of porting a matlab code and executing it on GPU and CPU, so that one can compare the performance and evaluate its enhancement by GPU.

  • Tue Aug 13, 1:00 pm - 3:00 pm
    Walter Library

    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.

    Prerequisites: Basic knowledge of Linux, rudimentary knowledge of a programming language

  • Thu Aug 8, 1:00 pm - 3:00 pm
    Walter Library

    This tutorial will briefly introduce MSI systems, remote access, and job submission systems, before giving a more detailed tour of hardware and software resources of particular utility to students and researchers in the physical sciences.

    Prerequisites: Basic knowledge of Unix-like systems and command line. Attendance at “Introduction to MSI” is helpful but not required, as that material will be covered in summary form only.

  • Tue Jul 30, 1:00 pm - 3:00 pm

    ProteinPilot™ is a proteomics software program used for analysis of peptide tandem mass spectrometry data and for relative quantification of proteins using the iTRAQ® technology and other modes of stable isotope labeling. Raw data acquired on a mass spectrometer such as Orbitrap-Velos is searched against protein sequence databases; the Paragon scoring algorithm provides confidence levels for protein hits, and the ProGroup algorithm tool (PMID: 17533153) groups related and homologous proteins.The tutorial will include an introduction to the software followed by iTRAQ® Data analysis workflow and FDR analysis overviews within Galaxy-P.

    This tutorial is a webcast utilizing UMConnect. Please register as usual. Registered users will receive meeting information by email within 24 hours of the start date. Please visit to ensure that your system meets the minimum requirements necessary to participate in this webinar.