This lecture will cover the basics of RNA-Seq experimental design and data quality assessment, followed by an overview of data analysis for the detection of differentally expressed genes. Specific subtopics include:
MSI has deployed a cloud service for research computing called Stratus. In its initial iteration, Stratus is designed expressly to satisfy the requirements set forth by the NIH Genomic Data Sharing (GDS) Policy for data from the Database of Genotypes and Phenotypes (i.e., dbGaP data).
This tutorial will help users learn the basics of parallel computation methods, including strategies for collecting calculations together for parallel execution. A brief description of parallel programming using MPI message passing will be given.
Introduction to common techniques for the analysis and quantitation of proteomics mass spectrometry ("mass spec") data. Topics covered will include the concept of Peptide-Spectra Matching (PSM) versus de novo sequencing, as well as the application of commonly used algorithms such as Andromeda (M
This tutorial will help users learn the basics of compiling and debugging their code on MSI systems. Particular attention will be paid to code written in Fortran, C, and C++. Basic methods for debugging will be outlined, with users being able to explore different debugging tools.
This two part tutorial will first introduce you to the concept of interactive high performance computing, as distinct from batch computing. We will cover the Citrix (Windows) and NICE EnginFrame (Linux) interactive computing environments hosted by MSI.
Intel will be providing training, to help software developers optimize their codes for the Xeon Phi coprocessor. This training is being held at the Minnesota Supercomputing Institute at the University of Minnesota. Current University students, staff, and faculty are invited.
Python is a modern general purpose programming language that is popular in scientific computing for its readable syntax and extremely rich ecosystem of scientific and mathematical modules.
If you are new to bioinformatics this is the best place to start.
This hands-on tutorial will help a new user understand how to use the the Galaxy platform to analyze NGS data by working though the quality control steps needed for Illumina sequencing data.