All Tutorials

  • Tue Oct 25, 1:00 pm - 3:00 pm
    Cargill Building

    Sequences evolutionary analysis is an important method for exploring the relatedness of species or proteins. There are many software tools that use different algorithms. PAUP (Phylogenetic Analysis Using Parsimony) is a widely used package for the inference of evolutionary trees. The new version 4.0 includes maximum likelihood, parsimony, and distance methods.

    In this tutorial, we will demonstrate the parsimony, maximum likelihood, and distance methods of PAUP using test sequence data.

  • Thu Oct 20, 1:00 pm - 3:00 pm
    Walter Library

    Genomics has changed the face of life sciences since the first draft of the human genome sequence was released in 2000. Computational tools play an important role in this change.

    The Supercomputing Institute has some of the most powerful computational genomics software tools available. These tools allow for genomics data acquisition, quality assessment, normalization, statistical analysis, functional annotation, pathway, interaction network, structural genomics, and data management.

    This tutorial will overview around 15 of the Institute/.s microarray and pathway genomics software tools and will guide users in accessing these resources.

  • Tue Oct 18, 1:00 pm - 3:00 pm
    Walter Library

    More and more biological studies involve collection and analysis of three-dimensional images varying over time, often called 4D images. IMARIS is an interactive volume visualization system for 3D and 4D biomedical data.

    This tutorial will introduce users to several features of the IMARIS modules Imaris Time, Imaris MeasurementPro, and ImarisColoc. It will demonstrate practical applications for image analysis, segmentation, object classification, quantitation, colocalization analysis, and tracking of biological structures in 2D, 3D, and 4D.

  • Thu Oct 13, 1:00 pm - 4:00 pm
    Walter Library

    Writing code is only the beginning of completing a programming project. It is rare for a code to be completed without a single bug. This workshop will present the debuggers available at the Institute and general techniques for finding bugs. TOTALVIEW has evolved into the most powerful debugging tool for serial and parallel applications written in C, C++ and/or FORTRAN. It supports multiple parallel programming paradigms including MPI and OPENMP.

    The aim of this hands-on workshop is to help users learn how to debug codes. Users will have a chance to learn through hands-on examples how to use the TOTALVIEW graphical user interface and the various features of TOTALVIEW to debug a serial code, MPI, OPENMP, and/or multithread applications.

  • Tue Oct 11, 1:00 pm - 3:00 pm
    Walter Library

    The SAS system is a collection of programs originally designed to perform statistical analysis of data. The SAS software started out in the 1970s as a package for statistical analysis. By the early 1980s, SAS had already branched out into graphics and spreadsheets. The SAS system now has a diverse family of products. Most of its products are integrated together and can be used as building blocks to construct a seamless system.

    MSI has the SAS system installed on its supercomputers. In this tutorial, we will cover some topics on multivariate data analysis, such as principal component analysis and canonical correlation analysis. We will also cover techniques to write a basic SAS code that can perform these analyses.

  • Thu Oct 6, 1:00 pm - 3:00 pm
    Nils Hasselmo Hall (NHH)

    Microscopic images are mostly collected as stacks (3D) and often with time lapses (the fourth dimension). Huygens is a comprehensive deconvolution package for 3D and 4D microscopy.

    This tutorial will introduce users to image processing algorithms for wide-field and confocal microscopes. It will demonstrate practical applications of Huygens in deconvolution, resolution, and noise reduction for restoring images. Users will also be introduced to batch utilities in Huygens Scripting (available at the Institute) to process large numbers of image datasets automatically.

  • Tue Oct 4, 10:00 am - 4:00 pm
    Walter Library

    This one-day workshop on MPI will help researchers write better and portable parallel codes for distributed-memory machines like Linux clusters. We 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 nonblocking communication will be introduced.

    The workshop will combine a lecture with hands-on practice. The lecture introduces basic principles, and the hands-on portion focuses on the use of MPI principles via examples.

    1. Introduction to basic concepts of "MPI Is Small", centering on point-to-point communication.

    2. MPI collective communications including: broadcast, gather, scatter, and Alltoall.

    Programming will be done in Fortran and C, so any background in these two languages will be helpful.

  • Mon Oct 3, 1:00 pm - 3:00 pm
    Cargill Building

    GCG Wisconsin Package, DS Gene, and MacVector are bioinformatics software from Accelyrs for use on UNIX, Windows, and Macintosh platforms. They can be used for sequence analysis, restriction enzyme mapping, primer selection, etc.

    This tutorial will introduce each of these packages and will cover the following topics:

    1. Overview

    2. Data and database files that the programs access

    3. How to get started

    4. Programs by function

  • Thu Sep 29, 1:00 pm - 2:00 pm
    Walter Library

    A Makefile provides a convenient and efficient way to build projects from source files. It is the de facto standard in the world of UNIX developers. The MAKE program allows you to manage the dependencies between various files composing the project, saving a very significant amount of time during code development by eliminating unnecessary recompiles.

    During this tutorial, the basics of MAKE will be presented for both simple and complex projects. A popular MAKE extension, GNU MAKE, will also be discussed.

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

    Statistics are very important to many scientific research projects. R and S-PLUS are powerful statistical computing languages and environments available at the Supercomputing Institute. Bell Laboratories developed the S language and environment in the 1980s for data analysis. S was further developed into a commercial product called S-PLUS. R is a dialect of the S language.

    This tutorial will demonstrate how to read and manipulate data in the R and S-PLUS environments. In addition, attendees will learn how to perform basic statistical analysis in R and how to produce graphics with the software packages.