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Wed Dec 14, 1:00 pm -
419 University Square
Galaxy (http://usegalaxy.org; http://galaxy.msi.umn.edu) is a bioinformatics workflow framework designed to provide a web interface to bioinformatics tools that are routinely used though generally accessed by command line. The ease with which users can share data and results, review analytical logs and create analytical pipelines contributes to the user-friendliness of the Galaxy tool. 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 has 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.
Access to galaxy.msi.umn.edu requires an active MSI account.
Thu Dec 8, 1:00 pm -
402 Walter Library
OpenFOAM is an open source software package which is designed to scale well on large distributed memory systems. While originally written for CFD, with its open source strategy and a large user base OpenFOAM has grown to be a general purpose finite element toolbox. This tutorial will cover the basics of using OpenFOAM to set up, solve, and view results for a variety of physical models. Techniques for running OpenFOAM on thousands of cores will be discussed. A hands-on session in 575 Walter will immediately follow this one-hour presentation.
Presentation: 1:00-2:00 in 402 Walter
Optional hands-on session: 2:15-3:15 in 575 Walter
Wed Dec 7, 1:00 pm -
575 Walter Library
ProTIP is a package of services that integrates analysis tools into the TROPIX framework. As part of the ProTIP project, standard analysis tools such as Sequest, X!Tandem, and Scaffold are executable from within the TINT graphical interface.
The tutorial will include a walk-through on using ProTIP and new features included in ProTIP.
Tue Dec 6, 1:00 pm -
The technology behind data acquisition and especially image acquisition have grown enormously over the years. Data sets of size greater than 1GB are common. Such datasets present a unique problem during the visualization process. They need large memory, powerful CPUs and good graphic capabilities in the form of graphics cards. Such technologies are expensive for individual researchers to buy and maintain, so MSI has been working on creating such an infrastructure.
In this tutorial, we will introduce the remote visualization capabilities of MSI. We will discuss the details of the various visualization systems users can access. We will also discuss the software, VirtualGL, for connecting to these systems.
This tutorial utilizes UMConnect and takes place entirely online. Please register as usual. Registered users will receive meeting information by email within 24 hours of the workshop start date. Please visit http://www.oit.umn.edu/umconnect/ to ensure that your system meets the
minimum requirements necessary to participate in this webinar.
Thu Dec 1, 1:00 pm -
575 Walter Library
MSI has a new high-performance computing system named Koronis. It features an SGI Altix UV 1000, one of the largest global shared memory (GSM) systems available. Koronis offers unprecedented opportunities for NIH researchers to conduct memory-intensive calculations. At the same time, it poses great computational challenges from the system-memory complexity that - combined with the flexibility in the selection of the number of computing cores - can severely degrade the performance. This tutorial will help Koronis users improve application performance. We will show examples of programs that can take advantage of this computer. We will also describe tactics that can be used in the calculations within the CPUset regime to achieve optimal performance.
Tue Nov 29, 1:00 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.
This tutorial serves varying interest groups ranging from medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.
Tue Nov 29, 10:00 am -
414 University Square
10 am - 12 am - Use of Matlab for computation
1 pm - 3 pm - Image processing and visualization using Matlab
Use of Matlab for computation
MATLAB is an integrated technical computing environment that combines numeric computation, graphics and visualization into a high-level programming language. MATLAB includes hundreds of functions for data analysis, numeric and symbolic computation, and scientific graphics modeling and simulation. This portion of the tutorial consists of (1) a 60-minute lecture describing the basics of using Matlab for computing and (2) a 60-minute hands-on session focusing on the use of the basic functions for your application.
Image processing and Visualization using Matlab
Matlab has powerful capabilities to perform 2D and 3D visualization. It also has the Image Processing Toolbox with hundreds of functions that can be used to perform operations on images.
First we will discuss the various 2D and 3D visualization functions. We will execute examples to cement the understanding.
We will then discuss image processing using Matlab. The various image processing operations can be classified into reading, processing and writing images. We will begin with reading and writing images. We will also discuss reading complex image formats like DICOM. We will then perform various image processing operations like filtering, visualization and analysis.
We will intersperse the lecture with hands-on exercises, so you can better understand the material. You are also welcome to bring specific questions and problems that you would like to discuss.
Tue Nov 22, 9:00 am -
138 Cargill Building
Illumina Genome Analyzer (GA) can generate up to 100 million
sequence reads per lane with 5 to 10 gigabase DNA sequences.
It has been widely used in biological research including
genome sequencing, gene expression analysis, variation
This tutorial will first introduce the new terminologies
and data types associated with Illumina genome analyzer.
Then we will discuss general strategies about data
analysis including sequence assembly, mapping, SNP
detection, and data visualization.
Thu Nov 17, 1:00 pm -
585 Walter Library
Microscope images are a complex dataset consisting of multiple structures and intensities spread across various channels. Hence, visualizing and analyzing this data becomes paramount.
Imaris helps in visualizing all standard microscope formats. It can also be used to create iso-surfaces, perform statistical analysis based on the pixel intensities and perform co-localization (identifying pixels and entities that are present in more than one channel.) In addition to these operations, it has other modules to perform specialized functions like movie generation, etc.
Tue Nov 8, 9:00 am -
138 Cargill Building
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 tool well-suited for biological data manipulation and analysis.
This tutorial will introduce the fundamental concepts and
mechanisms of Perl programming. We will use practical examples
to demonstrate how to write Perl codes to do transcription,
translation, batch sequence retrieval, promoter sequence
extraction from genomic DNA, motif scanning, query gene ontology
database, etc. Through these examples, you will learn how
Perl programming can make you work easier and more