• Galaxy
  • PBS Scripts
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  • Tutorials List

    Displaying 1 - 30 of 41
    Tutorial Name Summary Next Date Offeredsort descending
    Compiling and Debugging

    This tutorial will help users learn the basics of compiling and debugging their code on MSI systems

    10/08/2019
    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

    10/10/2019
    Parallel Computing Overview

    This tutorial will help users learn the basics of parallel computation methods, including strategies for collecting calculations together for parallel execution

    10/17/2019
    Singularity & Containers

    This course will introduce users to containers and provide hands-on experience running both interactively and within batch scheduled jobs.

    10/22/2019
    MPI

    This tutorial 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

    10/24/2019
    UMN Duluth: Introduction to MSI

    Description of MSI services including our access to our experts, HPC systems and storage options. Policies regarding computing resource usage and storage usage will be covered.

    10/25/2019
    UMN Duluth: Introduction to PBS scripts and Job Queues

    Hands on tutorial on how to write a PBS script and how to submit it to a queue. Queue limits and SU accounting will also be covered.

    10/25/2019
    UMN Duluth: Job parallelization with task arrays and GNU parallel

    Tutorial on how to use task arrays or GNU parallel to make use of the parallel computing environment at MSI.

    10/25/2019
    UMN Duluth: Illumina, Nanopore, and Pacific Biosciences technologies

    How these technologies can be used in a research program, and what questions they can address. Resources at MSI for analyzing these types of data.

    10/25/2019
    Python for Scientific Computing

    This session includes efficient data processing with NumPy and Scipy, data visualization, and techniques for using python to drive parallel supercomputing tasks.

    10/29/2019
    Rna-Seq Analysis

    This tutorial covers the basics of differential expression analysis and touches on other RNA-seq topics such as transcriptome assembly.

    11/05/2019

    This hands-on tutorial will help a new user understand how to use the the Galaxy platform to analyze NGS data

    N/A
    Introduction to Minnesota Supercomputing Institute (MSI)

    This tutorial is geared to new MSI users and will provide a highlevel introduction to the facilities and computational resources at MSI.

    N/A
    Job Submission and Scheduling

    This tutorial will introduce users to MSI supercomputers, and provide an overview of how to submit calculations to the job schedulers

    N/A
    Introduction to Linux

    This tutorial will provide an introduction to the Linux operating system, with particular attention paid to working from the command line

    N/A
    502 Bad Gateway

    This tutorial covers Intel Xeon Phi architecture, programming models, parallel frameworks, and optimization methods

    N/A
    Interactive Computing

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    N/A
    Abaqus

    This tutorial covers an overview of the new enhancements to Abacus as well as a brief introduction to Isight, Tosca, and fe-safe.

    N/A
    OpenMP

    This tutorial provides an introduction on how to write a parallel program using OpenMP, and will help researchers write better and more portable parallel codes for shared memory Linux nodes

    N/A

    502 Bad Gateway

    This tutorial focuses on command line tools in the Galaxy enviornment to analyze ChiP-Seq data, automate mapping and peak calling, and edit and run scripts.  

    N/A
    PacBio Sequencing - Lecture

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

    N/A
    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.

    N/A

    nginx

    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.

    N/A
    Quality Control of Illumina Data at the Command Line

    This hands-on tutorial will introduce new bioinformaticitions to the skills needed to start to build more complex analysis pipelines. 

    N/A
    Digital Gene Expression (DGE) Analysis Using Galaxy, Human Data

    This is a practical, hands-on tutorial designed to give participants experience with RNA-Seq data analysis using Tophat, Cufflinks, and CummRbund in Galaxy.

    N/A
    Analyzing ChIP-Seq Data using Galaxy

    This practical, hands-on tutorial is designed to give participants experience with ChIP-Seq data analysis using the Galaxy platform. 

    N/A
    Interacting with dbGaP data on Stratus

    This tutorial introduces Stratus to users who wish to process dbGaP data at MSI

    N/A

    (Lecture only) This tutorial is an introduction to common techniques for the analysis and quantitation of proteomics mass spectrometry ("mass spec") data.

    N/A
    Getting started with XSEDE resources

    This hands-on tutorial will introduce MSI researchers to multiple XSEDE resources.

    N/A
    Introduction to Deep Learning with Caffe and Tensorflow

    In this tutorial, MSI and Nvidia instructors will walk through an interactive exercise running programs such as Caffe and Tensorflow.

    N/A

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