All Tutorials

  • Thu Jul 16, 1:00 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 Jul 15, 9:00 am - 11:00 am
    575
    Walter Library

    GeneGo's unique bioinformatics technology for systems biology enables complete reconstruction of mammalian cellular functionality from interactions data at the level of ligand-receptor interactions, cell signaling and regulation and core metabolism. Whether you are working with one gene or an extensive list from high throughput data, learn how to tweak out the associated cellular functionality with Basic Training using MetaCore.


    In this training you will learn how to upload your gene list or build the list using MetaCore search tools, exploit the functional enrichment of a data set and build a network to depict these functional interactions. You will also learn how MetaCore allows for the comparison (1-2-3 step workflow) of several data sets to determine what biology is shared or unique to each. In addition, we will cover how to overlay and visualize expression levels of objects from the same data to help you formulate more applicable hypotheses.


  • Tue Jul 14, 1:00 pm - 3:00 pm
    575
    Walter Library

    Image manipulation includes such functions as cropping, rotating, resizing, adding text, photo retouching, color conversion, and much more. Image manipulation can be used when preparing photos for print or the web or when creating animation. MSI has several programs that can be used for image manipulation; this tutorial will introduce you to three of those programs.


    Adobe Photoshop is the most popular commercial package for image manipulation. ImageMagick is a free collection of programs to display, manipulate and convert images from one format to another. ImageMagick can be used from a GUI or from the command line. GNU Image Manipulation Program (Gimp) is a free, general image processing program for editing images.


    The tutorial serves varying interest groups ranging from medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


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

    GeneSpring is one of the most widely used microarray software programs for both one-channel and two-channel microarray data analysis. Besides the basic statistical methods, it shows strength in various normalizations, gene annotation and gene ontology analysis, and user-friendly visualizations.


    Using test data, we will demonstrate GeneSpring functions including genome installation, data loading, experiment creation, normalization, filtering, clustering, group comparisons, gene list Venn diagram, and gene ontology, class prediction tool, gene ontology, pathway, Scripts, etc.


  • Tue Jul 7, 1:00 pm - 3:00 pm
    585
    Walter Library

    MATLAB is one of the most practical software programs used for numerical calculations and system design. MATLAB applications, however, can run much more slowly than FORTRAN and C codes for the same kind of applications. MATLAB code debugging is also an unavoidable component of application development. This tutorial will teach users how to use MATLAB’s debugging and profiling tools in addition to the basic techniques to write efficient MATLAB codes.


    A hands-on practice will follow the lecture. We will provide examples to enable participants to use the debugging and profiling tools to write an efficient MATLAB code. You are also encouraged to bring in your application codes. The user support staff will help you debug your code and/or improve the code’s performance.


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

    Trying to discover patterns in data? Looking for techniques for classification and prediction? In this hands-on tutorial, we show you how to accomplish these data mining tasks using Weka. Weka is a freely available software package for knowledge analysis and pattern discovery that contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization.


    In this tutorial, we go through the basic steps involved in loading data into Weka, exploring and filtering data, and applying Weka data mining tools. The main focus is on techniques for classification, such as decision trees or neural nets, but we will also explore the other capabilities of Weka (clustering, association analysis, etc.) as time allows.


  • Thu Jun 25, 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 Jun 23, 1:00 pm - 3:00 pm
    402 and 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 one-hour, hands-on session focusing on the use of these functions for your application


  • Fri Jun 19, 9:30 am - 3:30 pm
    575
    Walter Library

    IPA is a web-based software application that enables you to analyze data derived from expression and SNP microarrays, proteomics experiments, and small-scale experiments that generate gene lists. It also enables you to search for targeted information on genes, proteins, chemicals, and drugs, as well as build your own biological models. With IPA, you can easily search the scientific literature for insights relevant to your experiment and quickly analyze your experimental data to identify key insights.


    This seminar is appropriate for scientists with or without experimental data. Topics covered will be of interest to therapeutic area researchers, biologists, clinicians, toxicologists and bioinformaticians alike.


  • Thu Jun 18, 10:00 am - 4:00 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 other 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.


    The Tutorial is broken up into two parts: a morning lecture from 10:00 to 12:00 in 402 Walter to demonstrate the basic functionality of the Schrodinger suite and a hands-on afternoon workshop in 575 Walter where users will get a chance to set up different models and use some of Schrodinger’s tools.


    If you would like a certain topic discussed in detail as part of workshop, please indicate what you would like to discuss in the comments section when you register.


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