All Tutorials

  • Thu Oct 16, 1:00 pm - 3:00 pm
    575
    Walter Library

    The Schrodinger software suite is a full-featured molecular modeling package designed to solve real world problems in pharmaceutical, biotechnology, and materials science research. One major advantage over other computational chemistry packages is that little to no text editing, scripting, or otherwise manual preparation of files is necessary to get started with the suite. This introduction to molecular modeling will focus on developing input and setting up calculations with the front-end GUI Maestro, various molecular mechanics and dynamics calculations, and the technical aspects of docking, quantum mechanics, and QM/MM studies.


  • Tue Oct 14, 1:00 pm - 3:00 pm
    402
    Walter Library

    Microarray is a powerful technology for biological exploration which enables users to simultaneously measure the level of activity of thousands of genes. It is becoming a routine experimental technique for life science research.


    This tutorial is an overview of this technology, which includes different microarray platforms, array design, data acquisition, data normalization, data analysis, and gene list interpretation. We will also introduce and compare several microarray software tools that MSI hosts.


  • Thu Oct 9, 1:00 pm - 3:00 pm
    575
    Walter Library

    Amira is a powerful visualization software package that enables data manipulation, geometry creation, and viewing in a meaningful format. This tutorial will describe the modular approach in Amira to build a visualization framework for different scientific data types. We will introduce concepts in computational geometry, modeling, and surfaces and volume rendering in Amira. This tutorial serves varying interest groups including medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


  • Tue Oct 7, 1:00 pm - 3:00 pm
    402
    Walter Library

    The SAS system started out in the 1970s as a software package for statistical analysis, but is now a diverse family of integrated products that can be used as building blocks for constructing a complete data analysis system for data sets ranging from small to very large. In this tutorial, we provide an introduction to SAS.


    Among other skills, we will learn to load, create, and combine data sets in different ways, generate random samples, post results on the Web, and make simple plots. We will also cover writing basic code, using common statements and functions in SAS, and using statistical procedures. This tutorial is appropriate for people who have data that need to be processed and analyzed statistically.


  • Thu Oct 2, 1:00 pm - 4:00 pm
    575
    Walter Library

    Python is a general purpose programming language with a rich syntax and structure. It also has many modules specializing in various topics of interest to the scientific community like mathematical and textual processing. It is additionally used as an interface for numerous scientific packages such as NWChem and the Schrodinger suite. This tutorial is divided into two parts. The first will focus on an introduction to programming with Python. Topics covered will include control structures, data types, functions, mathematical and logical operators, and program input and output. The second part of the tutorial will cover advanced topics in Python like issuing commands to the Unix shell, reading and writing spreadsheet files, creating XML documents, and performing mathematical operations like a Pythonista.


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

    The CCP4 suite is a collection of programs used in most of the computations involved in protein x-ray crystallography. The package includes programs for data processing, molecular replacement, MIR, structure refinement, and validation, as well as a graphical user interface for most of the common programs.


    This tutorial will give an overview of the suite and its use, as well as a detailed description of how to run the program here at MSI, including how to run some of the basic programs initially used in refining protein structures like Molrep and Refmac.


  • Tue Sep 30, 1:00 pm - 3:00 pm
    402
    Walter Library

    EMBOSS (European Molecular Biology Open Software Suite) is a free open-source package designed for the needs of the molecular biology community. Currently, EMBOSS has approximately 100 applications that cover several areas of molecular biology: sequence alignment, database searching, protein motif identification, and many others.


    This tutorial will cover an overview of software, file and database for EMBOSS, DNA sequence analysis and protein sequence analysis, protein primary and secondary structure, etc.


  • Thu Sep 25, 10:00 am - 4:00 pm
    575
    Walter Library

    This one-day workshop on MPI will help researchers write better and portable parallel codes for distributed-memory machines like Linux clusters, such as MSI?s IBM Power4, SGI Altix, BladeCenter and Calhoun. It 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 introduces basic principles, and the hands-on portion focuses on the use of MPI principles via examples. Session One: Introduction to basic concepts of "MPI is Small," centering on point-to-point communication. Session Two: 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.


  • Tue Sep 23, 1:00 pm - 3:00 pm
    402
    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 one-hour, hands-on session focusing on the use of these functions for your application.


  • Thu Sep 18, 10:00 am - 4:00 pm
    575
    Walter Library

    OpenMP is a parallel programming interface for shared-memory architectures and is available on the IBM Regatta and the SGI Altix. This one-day workshop will help users to use OpenMP programming more productively for high-performance computing by addressing the different aspects of OpenMP, such as parallel and work sharing constructs, data scope attribute clauses, and synchronization constructs. In addition, the new features in the OpenMP II standard will be covered.


    A hands-on practice will follow the lecture. Provided examples will enable the users to insert OpenMP directives for different parallel tasks and data scope attribute clauses. The users are also encouraged to bring in their serial application codes. User Support staff will help you parallelize the code with OpenMP.


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