All Tutorials

  • Thu Sep 17, 8:30 am - 5:00 pm
    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 ( 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 for more information.

  • Wed Sep 9, 1:00 pm - 3:00 pm
    Walter Library

    MSI is hosting an ANSYS presentation and demo of the new FLUENT R12 release. Laz Foley from ANSYS will give an overview and demonstrations of this new software and will be available for answering questions.

    Special topics will include

    * New ANSYS Workbench Interface including:

    - Bi-directional CAD associativity

    - Geometry Modeling

    - ANSYS Meshing Platform

    * Fluent Solver Update

    * New Post Processing

    * Parameter-driven analysis & Goal-driven Optimization

    * One-way Fluid-Structure Interaction

    This will be an interactive session, and time will be spent on the topics that are of most interest to the attendees.

    Registration is not required. However, it would be helpful if you do register and provide comment on which topics will be of particular interest to you.

  • Thu Aug 6, 1:00 pm - 3:00 pm
    Walter Library

    TROPIX is set of caGrid web services designed to improve the flow of data from core laboratories. It can be used to share arbitrary data with user-defined groups using the TINT web interface at MSI. TROPIX is also a building block from which one can integrate analytical services, such as ProTIP, to analyze data.

    ProTIP offers an integrated solution for proteomics data analysis by utilizing resources that are available at MSI. ProTIP can be used to extract peaklists from raw data and submit these peaklists for searches to search algorithms like Sequest, X!tandem and OMSSA. The search results from these search algorithms can be further processed by using Scaffold. Moreover, search results from Mascot can also be integrated into the Scaffold workflow.

    This tutorial will introduce you to the basic structure of TROPIX and ProTIP, followed by a tutorial on setting up searches using multiple search algorithms through ProTIP. Results from earlier analyses will also be discussed during the tutorial.

  • Tue Aug 4, 1:00 pm - 3:00 pm
    Cargill Building

    The Genome Sequencer (GS) FLX Titanium from Roche/454 is an ultra high-throughput instrument for conducting nucleotide sequencing. It potentially can generate one million sequencing readings with an average reading at about 400 nucleotides long within a single operation run. This tutorial will introduce the principles of 454 sequencing technology, potential applications, data types, and data analysis. The main focus will be GS de novo Assembler, GS Mapper, and GS Amplicon Variation Analyzer.

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

    The Timelogic DeCypher system implements configurable-computing technology in a unique hardware and software system. It dramatically accelerates computationally intensive bioinformatics algorithms, including BLAST, Smith-Waterman, and HMM analysis.

    This tutorial will first introduce the web interface to the Timelogic DeCypher system. Then we will focus on the Command Line Interface (CLI) to Timelogic Decypher, including how to create a target database, submit a search job, and retrieve results.

  • Tue Jul 28, 1:00 pm - 3:00 pm
    Walter Library

    MATLAB is a software package for technical computing. Its well-designed user interface, easy-to-use programming language, and wide range of mathematical, statistical, and simulation capabilities have made it a standard in many technical communities. This hands-on tutorial provides an introduction to data mining with MATLAB for users who have a basic familiarity with the program. Topics to be covered include classification, clustering, neural networks, and regression. We will also discuss how to read data into MATLAB, from both text and Excel files, and demonstrate some of MATLAB’s extensive visualization capabilities.

  • Thu Jul 23, 1:00 pm - 3:00 pm
    Walter Library

    Proteomics is emerging as a powerful screening methodology for research in academic institutions and industry. A new generation of mass spectrometers with higher sensitivity and mass accuracy are now able to explore deeper into a proteome. Moreover, various methods are employed for quantitative analysis (such as iTRAQ, ICAT, SILAC, ExacTag, TMT, and spectral counting) that enable a researcher to measure comparative changes in a proteome for two or multiple samples simultaneously. All these developments have resulted in an increase in the data that is generated, which presents potential challenges for data processing of complex datasets.

    This tutorial will offer an overview of proteomics workflow, with a focus on data analysis using various software programs available at MSI.

  • Tue Jul 21, 10:00 am - 4:00 pm
    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, the new features in the OpenMP II standard will be covered.

    A hands-on practice will follow the lecture. The examples we provide will enable you to insert OpenMP directives for different parallel tasks and data scope attribute clauses. You are also encouraged to bring in your serial application codes. The user support staff will help you parallelize the code with OpenMP.