All Tutorials

  • Wed Oct 28, 10:30 am - 12:00 pm
    402
    Walter Library

    Computational modeling of proteins is a complex task, and there are many computational tools out there to answer many types of questions. The goal of this lecture is to give those not familiar with the tools of protein molecular mechanics an idea what tools are available in the field and what kind of questions they can help answer.


    This tutorial will touch on a wide array of computational techniques used to model protein structure, including Energy Minimizations, homology modeling, Monte Carlo simulations, and various types of Molecular Dynamic simulations, and will discuss what kind of information can be gathered from such techniques.


  • Tue Oct 27, 1:00 pm - 3:00 pm
    575
    Walter Library

    EnSight is a post-processing package for scientific and engineering data. EnSight provides a set of tools to help with many types of analysis, visualization and communication. With EnSight you can create contours, isosurfaces, particle traces, vector arrows, elevated surfaces, profile plots and much more. Ensight also supports animation and VR.


    Dave Baumgartner, Senior Software Developer from CEI, makers of Ensight, will be presenting the Ensight tutorial. There will be an opportunity for you to speak directly with Dave about your research projects. If you would like to see a particular topic included in the tutorial or would like to schedule time to speak with Dave, contact Nancy Rowe at rowe@msi.umn.edu.


  • Thu Oct 22, 1:00 pm - 3:00 pm
    575
    Walter Library

    Understanding the regulatory mechanisms of gene expression is the major function of genomics. The Trans/Cis-regulatory elements are regions of DNA or RNA that regulate the expression of genes. Except the experimental discovery, many bioinformaticians have developed various algorithms for predicting transcriptional regulatory mechanisms from the sequence, gene expression and interaction data. MSI has several such tools and databases for Trans/Cis-regulatory element analysis.


    This tutorial will introduce tools for Trans/Cis-regulatory element analysis including Transfac, MEME, Hmmer, and Bioprospector, and will demonstrate their use using sample sequence data.


  • Wed Oct 21, 1:00 pm - 3:00 pm
    575
    Walter Library

    Statistics plays a key role in many scientific research projects. Increasingly, the R statistical platform is being used to perform such analysis. R, an open source version of the S statistical language developed by Bell Laboratories in the 1980s, together with its commercial offshoot, S-PLUS, are powerful computing environments and languages for statistical computing and graphics.


    More specifically, these software packages provide capabilities for reading a wide variety of data formats, performing simple and sophisticated data manipulations, applying statistical tests and computations, and graphing the data and the results of the statistical analysis.


    This tutorial will demonstrate how to log in to MSI’s computers to get started with R and S-PLUS and how to read and manipulate data in the R and S-PLUS environments. In addition, attendees will learn to perform basic statistical analysis in R and to produce graphics. Both R and S-PLUS run on a wide variety of UNIX platforms, Windows and Mac OS. They are available on the computers at MSI, including the supercomputers, providing an ideal platform for long run-time and/or large memory R or S-Plus applications.


  • Tue Oct 20, 1:00 pm - 3:00 pm
    402
    Walter Library

    Python is a general purpose programming language with a rich syntax and structure. It has many modules specializing in various topics of interest to the scientific community such as mathematical and textual processing. Further, it serves as an interface for a huge number of scientific applications which have modules written in Python, are developed entirely in Python, or are extended and controlled with Python. This tutorial is divided into two components. An introduction to programming with Python covers control structures, data types, functions, mathematical and logical operators, and program input and output. The second part of the tutorial will address several special topics such as issuing commands to the UNIX shell, reading and writing spreadsheet files, creating XML documents, and performing mathematical operations like a Pythonista.


    This tutorial will be webcast. See https://www.msi.umn.edu/support/materials.html for more information.


  • Tue Oct 13, 10:00 am - 4:00 pm
    575
    Walter Library

    This one-day, hands-on workshop will introduce 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 One: Introduction to basic concepts of MPI, centering on point-to-point communication.


    Session Two: 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 Oct 6, 1:00 pm - 3:00 pm
    402
    Walter Library

    With the development of genomics and proteomics, many biologists now need to handle large amounts of data for their research. Bioinformatics programming, especially Perl programming, is a well-suited tool for biological data manipulation and analysis.


    This tutorial will introduce the fundamental concepts and mechanisms of computer programming. We will use practical examples to demonstrate how to write the Perl codes to do transcription, translation, batch sequence retrieval, promoter sequence extraction from genomic DNA, motif scanning, queries of gene ontology databases, etc. Through these examples, you will learn how bioinformatics programming can make your work easier and more efficient.


    This tutorial will be webcast. See https://www.msi.umn.edu/support/materials.html for more information.


  • Thu Oct 1, 1:30 pm - 3:00 pm
    402
    Walter Library

    PyMOL is a free-for-academic-use modeling software program useful for viewing and creating figures and animation of protein models. This tutorial is designed to help users learn how to navigate and view protein models in PyMOL with the goal of making simple figures and animations for presentations and publications.


  • Wed Sep 30, 1:00 pm - 3:00 pm
    575
    Walter Library

    MATLAB is an integrated technical computing environment that combines numeric computation, graphics and visualization, and a high-level programming language. MATLAB includes hundreds of functions for data analysis and visualization, numeric and symbolic computation engineering, and scientific graphics modeling and simulation.


    This tutorial consists of two parts:


    1. A 90-minute lecture describing the use of computation and visualization functions and tools.


    2. An optional 30-minute, hands-on session focusing on the use of these functions for your application.


  • Tue Sep 29, 1:00 pm - 3:00 pm
    125
    Walter Library

    The LMVL is a large-screen visualization system capable of immersive visualization with 3D stereo projection and motion tracking. The system can be run as a large desktop enabling users to easily view their data in 3D stereo with software they already use on their desktop systems. The system can also be used to display high-resolution images. The screen is 28 feet wide by 7.5 feet high and can display a resolution of 7680 x 2048 in high resolution.


    This tutorial will teach users how to access the system and how to use the system in both stereo mode and high-definition mode. We will cover the software programs currently being used in the lab, the control system, motion tracking, etc.


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