All Tutorials

  • Wed Nov 20, 1:00 pm - Thu Nov 21, 4:00 pm
    575
    Walter Library

    This two day tutorial (held from 1:00pm to 4:00pm on both days, Nov 20 & 21) covers topics typical of sequencing experiments in eukaryotic species with high-quality genomes and genome annotation available. Participants are expected to be familiar with next-generation sequence data and basic theory of variant detection.

    Participants will perform analyses from start to finish with the goal of identifying SNP variants using data from a de-identified human DNA sample. This will include (1) sample QA/QC, (2) mapping via BWA, (3) post-processing of alignment files to remove PCR duplicates, re-calibrate basecalls and cleanup regions near indels, (4) genotype calling, (5) SNP annotation, and (6) SNP filtering and quality re-calibration.


  • Thu Nov 7, 2:30 pm - 4:00 pm
    585
    Walter Library

    In this tutorial/webinar by nVidia, Application codes that will be covered include,


    • NAMD

    • GROMACS

    • Amber

    • LAMMPS

    • Desmond

    • HOOMD-Blue

    • GAMESS

    • Gaussian

    • NWChem

    • Octopus

    • Quantum Espresso

    • ParaChem

    • VASP

    Tutorial Attendees:

    If you plan on attending the tutorial then please register for it.


    Webinar Information:

    If you plan on attending the webinar ONLY, here is meeting information,



    -------------------------------------------------------
    Meeting information
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    Topic: GPU-accelerated MD & QC
    Date: Thursday, November 7, 2013
    Time: 12:30 pm, Pacific Standard Time (San Francisco, GMT-08:00)
    Meeting Number: 621 179 241
    Meeting Password: Gpumdqc1
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    To start or join the online meeting
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    Go to https://nvidia.webex.com/nvidia/j.php?ED=269739747&UID=498387272&PW=NMWVkMDAxNDc2&RT=MiM0
    -------------------------------------------------------
    Audio conference information
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    Toll-free dial-in number (U.S. and Canada): (800) 214-4489, x7690906#
    International dial-in number: (404) 410-4582, x7690906#
    Conference code: 7690906#
    -------------------------------------------------------
    For assistance
    -------------------------------------------------------

    1. Go to https://nvidia.webex.com/nvidia/mc

    2. On the left navigation bar, click "Support".

    To add this meeting to your calendar program (for example Microsoft Outlook), click this link:
    https://nvidia.webex.com/nvidia/j.php?ED=269739747&UID=498387272&ICS=MS&LD=1&RD=2&ST=1&SHA2=DqLDJxN0AZF7n4hTvIu71ZVhLZe9Lkukm9PPKLtuw3w=



    To check whether you have the appropriate players installed for UCF (Universal Communications Format) rich media files, go to https://nvidia.webex.com/nvidia/systemdiagnosis.php.
    http://www.webex.com



    IMPORTANT NOTICE: This WebEx service includes a feature that allows audio and any documents and other materials exchanged or viewed during the session to be recorded. You should inform all meeting attendees prior to recording if you intend to record the meeting. Please note that any such recordings may be subject to discovery in the event of litigation.


  • Thu Nov 7, 1:00 pm - 4:00 pm
    575
    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.


  • Wed Nov 6, 9:00 am - 11:00 am
    402
    Walter Library

    DNA resequencing with the intent to identify single nucleotide polymorphisms in individual samples is emerging as a frequent core task to identify genotypic differences in a population that may contribute to important phenotypic effects. The computational field has converged on a standardized best practices suite of tools for analyzing this type of data centered around the Genome Analysis Toolkit (GATK). This lecture-style tutorial will cover the background material necessary for investigators who are just entering the field, and will serve as a good introduction to the more in-depth hands-on tutorial that follows.


    General topics covered will include: Basic background on Next-Generation Sequencing (NGS) DNA-Seq experimental protocols and data formats (e.g., fastq, SAM, BAM, VCF), overview of high-level project strategies (e.g., whole genome resequencing, hybridization capture, amplicon sequencing approaches, and pooling strategies), fundamental steps in analysis, design concerns and recommendations for different organism characteristics (e.g., diploid bi-allelic, polyploid, aneuploid, multi-allelic) and internal and external resources for subsequent consultation.


  • Tue Nov 5, 1:00 pm - 3:00 pm
    575
    Walter Library

    MATLAB is a general computational platform for rapid development of programs. It also has several toolboxes that allow specialized computation on images. One such toolbox, the Image Processing Toolbox, has hundreds of functions that can be used to perform operations on images.


    The various image processing operations can be classified into reading, processing and writing images. We will begin the tutorial by performing simple image reading operations on jpeg, gif, etc. We will also discuss reading complex image formats like DICOM. We will then perform various image processing operations like filtering, visualization and analysis. We will output these images to different formats to be read by other applications.


    Finally, we will conclude with hands-on practice using various example images. You are also welcome to bring specific questions and problems that you would like to discuss.


  • Thu Oct 31, 9:00 am - 4:00 pm
    575
    Walter Library

    Python is a general purpose programming language with a rich syntax and structure. You can learn to use Python and see almost immediate gains in productivity relative to programming with other languages. Python has many modules specializing in various topics of interest to the scientific community and is used as an interface for numerous scientific packages.


    The morning section will provide an introduction to Python. Simple and advanced data types, variable assignment, control structures, mathematical and logical operators, program input and output, and functional programming will be discussed.


    The afternoon section will cover advanced features of Python relevant to high performance computing. Topics will include efficient data processing with NumPy, integrating compiled routines into python programs, and techniques for using python to drive parallel supercomputing tasks.


  • Tue Oct 29, 1:00 pm - 3:30 pm
    575
    Walter Library

    In the second workshop on GPU computing, more attention will be on the use of multi-GPUs for accelarating Matlab applications under the parallel computing toolbox (PCT). We will teach attendees how to distribute different (independent) portions of an application onto different GPU devices on a compute node and how to use MATLAB/CUDA interface to run some existing CUDA/C++ code.

    A hands-on practice will follow the lecture. Provided examples will enable the attendees to get direct experience of executing tests on GPU and CPU, and appreciating the performance enhancement.


  • Tue Oct 29, 9:00 am - 4:00 pm
    402
    Walter Library

    Presented by:

    Xiaowen Wang, Field Application Specialist, Partek Inc.



    Partek will hold a one-day workshop at the University of Minnesota's Minneapolis Campus, October 29th. Please join us to learn how to perform comprehensive analysis of your Next Generation Sequencing and Microarray data and get the most biologically relevant results using our start-to-finish Partek solution!


    Morning Session (9:00am – 12:00pm, Conference Room 402 Walter Library): Upstream analysis on NGS data in Partek Flow.

    During this session, we will provide an overview of the functionalities of Next Generation Sequencing data analysis in Partek Flow. Partek Flow is a web-based application that has data and task manager specifically designed for NGS data analysis. Partek Flow takes raw sequencing data and uses them for QA/QC, alignment, SNP calling, gene fusion detection, and quantification & differential gene expression detection. The data smart interface guides you to build your analysis pipelines. All the resources and analysis pipelines can be shared. We will also demonstrate an RNA-Seq data analysis pipeline in Partek Flow starting from raw sequencing data to a differential expressed gene list.


    Afternoon Session One (1:00pm – 2:00pm, Conference Room 402 Walter Library): Hands-on RNA-Seq data analysis in Partek Genomic Suite.

    Partek Genomic Suite uses aligned data files. During this session, we will start with importing .bam files, perform QA/QC, estimate gene abundance and detect differential expression, and follow with biological interpretation. Visualizing data using PCA Scatterplot, dot plot, genome browser, and heatmap will be demonstrated during this session as well.


    Afternoon Session Two (2:15pm – 4:00pm, Computer Lab 585 Walter Library): Advanced Session, Open Lab, Q&A


    NOTE: Participants are strongly encouraged to bring their own laptops to the tutorial.


    Thank you for your interest and time. We are looking forward to seeing you there!


  • Thu Oct 24, 1:00 pm - 3:00 pm
    575
    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.


  • Tue Oct 22, 1:00 pm - 4:00 pm
    138
    Cargill Building

    This is a practical, hands-on tutorial designed to give participants experience with RNA-Seq data analysis using Tophat and Cufflinks in Galaxy. The analysis in this tutorial is typical of experiments in plant species with adequate quality genomes and genome annotation. Participants are expected to be familiar with next-generation sequence data and basic theory of RNA-Seq. Participants do not need previous experience with Tophat or Cufflinks.

    Prerequisites include: GALAXY 101 or experience with GALAXY and the Galaxy RNA-Seq Lecture.


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