All Tutorials

  • Thu Apr 28, 1:00 pm - 3:00 pm
    402
    Walter Library

    Homology modeling, or comparative modeling, is a process used to produce an atomic model of a protein structure when an experimental model does not exist. This is done by using a protein with a known structure and a similar primary sequence to the protein of interest to build a model. This method can be very useful in certain cases, but is very reliant on the quality of the sequence alignment and the template structure chosen as a basis for the model.


    This lecture will cover the basic theories and pitfalls of using homology modeling to generate protein models, as well as what MSI has to offer in terms of software packages that you can use to make comparative models of your proteins.


  • Thu Apr 28, 1:00 pm - 3:00 pm
    397
    University Square

    High-throughput technology such as microarray and next-gen sequencing makes it feasible to discover sequence or gene variations among the whole genome of a population. These variations could contribute to the phenotypic differences of the population such as variable disease susceptibility, environmental resistance, product yield, etc. The method used to correlate the genome-wide scope variations that are associated with these phenotypic differences is called a genome-wide genetic association study.


    This tutorial will discuss the strategies for a genome-wide genetic association study and the useful software tools for this study. We will also discuss the challenges and problems in genome-wide genetic association analysis.


  • Tue Apr 26, 1:00 pm - 3:00 pm
    575
    Walter Library

    Galaxy (http://usegalaxy.org) is a bioinformatics workflow framework that provides a Web interface to command line bioinformatics tools and enables sharing of data and tools between users. Within this framework, biologists can carry out a variety of computational analyses including gene expression profiling or RNA-seq, the focus of this tutorial. RNA-seq is quickly supplanting microarray technologies as the method of choice for transcriptomics. Tutorial participants will learn about the distinct computational issues that arise in applications where the reference genome has been sequenced versus cases where no reference genome is available. Strategies and workflows will be analyzed for each case, and participants will receive hands-on experience using state-of-the-art algorithms within Galaxy to obtain normalized transcript abundance counts from the raw sequenced reads. For more information about galaxy, visit http://galaxy.msi.umn.edu/home or view a Galaxy video tour at http://www.openhelix.com/galaxy


  • Thu Apr 21, 1:00 pm - 3:00 pm
    402
    Walter Library

    The Python programming language has been increasingly used for a wide variety of mathematical and statistical applications, even replacing MATLAB in some cases. In this tutorial we will introduce SciPy, NumPy and Matplotlib, three Python libraries that provide scientific, numerical, and plotting capabilities, respectively. SciPy uses Numpy to do advanced mathematics such as numerical integration, linear algebra, fft, signal processing, optimization, data mining, statistics, and more. Matplotlib can be used to produce publication quality plots such as those produced by MATLAB. We will also briefly introduce Python extension modules for using the R programming environment. We will cover how to write code using these packages and how to run the code on MSI machines.


  • Tue Apr 19, 1:00 pm - 3:00 pm

    This webinar combines elements from both the Introduction to MSI and Introduction to UNIX workshops to provide general assistance to new users getting started at MSI. It includes an introduction to MSI resources and a technical demonstration of commonly used UNIX tools and features.


    This tutorial utilizes UMConnect and takes place entirely online. Please register as usual. Registered users will receive an email with the meeting information within 24 hours of the workshop start date. To participate in the hands-on portion of the workshop, users must have access to an ssh command line tool (Putty on Windows, Terminal on Mac). Please visit http://www.oit.umn.edu/umconnect/ to ensure that your system meets the minimum requirements necessary to participate in this webinar.


  • Tue Apr 19, 9:00 am - 11:00 am
    397
    University Square

    Because of the extremely high volume of data generated by the Illumina/Solexa sequencing instrument, computational and bioinformatics skills are needed to handle data and perform data analysis.


    This hands-on tutorial will help users get started with data analysis for Illumina sequencing data. We will use sample data sets to walk through the basic steps, including converting qseq files into fastq files, quality control of sequence data, de novo sequence assembly with velvet and abyss, alignment/mapping with bowtie and maq, etc.


  • Thu Apr 14, 1:00 pm - 3:00 pm
    575
    Walter Library

    Galaxy (http://usegalaxy.org) is a bioinformatics workflow framework that provides a Web interface to bioinformatics tools that are routinely used and accessed by command line. In addition, Galaxy also enables sharing of data and tools and analytical workflows between users. Within this framework, biologists can carry out a variety of computational analyses including meta-genomics, gene expression profiling (RNA-seq), selective re-sequencing (ChIP-seq), and Next Generation Sequencing (NGS) sequence data manipulations, without needing any programming skills. Statistical tools are also available through Galaxy. Initially developed at Pennsylvania State University, this international open source platform was adopted by the University of Minnesota as the informatics component of the Minnesota partnership HAITI (High throughput sequence Analysis Infrastructure Technology Investigation) project and implemented at MSI. Galaxy is poised to become a key informatics resource for University of Minnesota researchers. In this tutorial, participants will become familiar with the layout of Galaxy, the scope of the tools provided, getting data into and out of Galaxy, the execution of selected tasks, the creation and manipulation of workflows, the modification of histories and their attributes, the sharing of data, workflows and histories with other users, and visualizing genomic tracks of information. For more information about Galaxy, visit http://galaxy.msi.umn.edu/home or view a Galaxy video tour at http://www.openhelix.com/galaxy


  • Thu Apr 7, 1:00 pm - 3:00 pm
    575
    Walter Library

    MATLAB is a general computational platform for rapid development of programs. It also has several toolboxes that allow specialized computation on images. One such toolbox, the Image Processing Toolbox, has hundreds of functions that can be used to perform operations on images. The various image processing operations can be classified into reading, processing, and writing images. We will begin the tutorial by performing simple image-reading operations on jpeg, gif, and other formats. We will also discuss reading complex image formats like DICOM. We will then perform various image processing operations like filtering, visualization and analysis and will output these images to different formats to be read by other applications.


  • Tue Apr 5, 1:00 pm - 3:00 pm
    575
    Walter Library

    Genotyping refers to the process of determining the genotype of an individual by sequence information. Different genotypes may be associated with specific phenotypes; therefore, genotyping can be used for genetic associated disease studies, drug-resistance association studies, high-yield gene mapping or plant strain selection.


    There are various methods available for genotyping. Recently, high-performance genotyping methods such as bead-based genotyping and next-generation sequencing genotyping have emerged. Moreover, there are different platform technologies available for array-based genotyping such as Affymetrix GeneChip, Illumina beadsArray, and Sequenom MassARRAY. This tutorial will compare these platforms in technical design and in their application. We will also demonstrate the use of software such as Affymetrix Genotyping Console™ (GTC), Illumina GenomeStudio, and Sequenom TyperAnalyzer by using sample data.


    This tutorial will also introduce the genotyping software hosted in MSI including Illumina GenomeStudio, Genotyping Console™ (GTC) Software, GeneMapper, Sequenom Typer, Matlab Bioinformatics toolbox for SNPs, dChip, SOAP, GeneSpring 11, and Bioconductor for SNP.


  • Thu Mar 31, 1:00 pm - 3:00 pm
    575
    Walter Library

    This tutorial will discuss the queue structure of MSI’s core resources and provide the information you need to write efficient PBS scripts that minimize your wait time and maximize job throughput. Topics covered will include batching many jobs to run in one script, writing automated loops in your PBS script, accessing useful environmental variables set by the scheduler, and an overview of tools available to you for monitoring job progress.


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