All Tutorials

  • 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.


  • Thu Sep 24, 10:00 am - 4:00 pm
    575
    Walter Library

    OpenMP is a parallel programming interface for shared-memory architectures and is available on all the core clusters. This one-day workshop will help you 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, we will cover the new features in the OpenMP II standard.


    Hands-on practice will follow the lecture. Users will learn to insert OpenMP directives for different parallel tasks and data scope attribute clauses. You are also encouraged to bring in your serial application codes. MSI user support staff will help you parallelize the code with OpenMP.


  • Wed Sep 23, 1:00 pm - 3:00 pm
    575
    Walter Library

    This is a hands-on workshop introducing relational databases and structural query language (SQL). Attendees will practice creating and querying databases in an Oracle environment. Topics include a brief overview of relational database design concepts and principals, and conceptual data models and constraints.


  • Tue Sep 22, 1:00 pm - 3:00 pm
    575
    Walter Library

    Perl is a scripting language that can make writing and maintaining scripts for various UNIX tasks considerably easier than trying to use one of the many shell languages. Perl is very useful, for example, for retrieving output from files of completed jobs for use in reports, input to subsequent jobs, and so forth. This hands-on tutorial will introduce users to the basic syntax, some powerful capabilities, and tools to keep your code manageable and readable by others.


  • Thu Sep 17, 8:30 am - 5:00 pm
    575
    Walter Library

    In this workshop Schrodinger scientists will present a brief overview of recent research and newly implemented software features, followed by training for their suite of drug discovery software. Topics to be covered include docking, post-docking analysis, workflow automation, and a "molecular spreadsheet" tool for cheminformatics calculations. Homology modeling and new methods of predicting relative free energies of ligand binding may also be covered if time permits.


    8:30 - 8:45 Introductory remarks


    8:45 - 9:15 Basics of the Maestro interface


    9:15 - 9:30 Break


    9:30 - 10:15 Target and ligand library preparation


    10:15 - 11:15 Docking


    11:15 - 12:00 Post docking analysis


    12:00 - 1:00 Lunch break


    1:00 - 2:00 Presentation: Overview of Schrodinger research and development projects


    2:00 - 2:15 Break


    2:15 - 3:00 Workflow automation with KNIME


    3:00 - 3:45 Introduction to cheminformatics with Canvas


    3:45 - 4:00 Break


    4:00 - 5:00 Presentation: Effect of Epik state penalties on Glide docking results


  • Wed Sep 16, 9:30 am - 2:30 pm
    402 and 585
    Walter Library

    On Wednesday, September 16, MSI will be giving a two-part seminar by Dr. Doug Robinson, a JMP Genomics Application Scientist from SAS/JMP. The morning presentation will provide an introduction to digital transcription profiling and its analysis in JMP Genomics. The afternoon presentation will provide a hands-on session on JMP Genomics. Please contact Haoyu Yu (Haoyu@msi.umn.edu) if you would like to discuss any topics with Dr. Robinson or see any particular topics presented, especially for the afternoon session.


    The morning session will be from 9:30-11:30 in 402 Walter Library. The title and abstract are presented below.

    The afternoon session will be from 1:00-2:30 in 585 Walter Library.


    Analysis of Next-Generation Schizophrenia Data: From Transcript to Exon


    Doug Robinson, Ph.D., JMP Genomics Application Scientist


    Digital transcription profiling is gaining in popularity due to the quality and quantity of information from a single assay. In this seminar we will present/demonstrate how JMP Genomics software can be used to analyze digital transcription profiling at both the transcript level and the exon level. Topics included are data transformation and formatting, quality control analysis, and mixed-model analysis of variance. In addition, for analysis of data at the exon level, we will show how mixed-model estimate values can be used to examine differences at the exon level either by group or by individual.


    Other tools within JMP Genomics that can be used with next-gen data will also be discussed, including copy number variance tools, cross-correlation tools and biomarker discovery/predictive modeling tools. This wide variety

    of analytical tools in a single software suite greatly simplifies the analysis of next-gen data sets.


  • Tue Sep 15, 1:00 pm - 4:00 pm
    402 and 575
    Walter Library

    This tutorial will offer a general introduction to the UNIX operating system followed by a hands-on session for using UNIX. The tutorial will also include an introduction to MSI resources with a brief overview about the hardware and software resources available and how to access these resources.


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


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