This tutorial will introduce users to MSI supercomputers, and provide an overview of how to submit calculations to the job schedulers. Topics covered include creating job scripts, types of jobs, job queues, differences in available hardware, checking job status, and choosing an appropriate place to submit a calculation.
This tutorial will provide an introduction to the Linux operating system, with particular attention paid to working from the command line. The tutorial will cover basics such as fundamental commands, editing files, understanding directories and permissions, and remote access. No previous Linux experience is required.
Deep Learning has emerged as an important new tool for a range of research applications. Emerging programs such as Caffe and Tensorflow are available at MSI and can be executed on Nvidia GPU resources. In this tutorial, MSI and Nvidia instructors will walk through an interactive exercise running some of these programs. Participants will be able to login to a node with a GPU to work through introductory exercises. We will also show how to run these programs in batch jobs on MSI systems.
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 (Maxquant), Comet (Sequest), and Mascot. Key parameters for different search engines will be discussed along with the statistical significance of their respective outputs. Statistics for these data types - and how quantitation can be done for different experimental setups - will be discussed in the
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 introduces Stratus to users who wish to process dbGaP data at MSI, and gives them an interactive lesson on how to access the service, deploy their first virtual machines, and move data through multiple tiers of storage.
Want to take your analysis to the next level?
This hands-on tutorial will introduce new bioinformaticitions to the skills needed to start to build more complex analysis pipelines. This tutorial will take you though the steps needed to run standard quality control analysis on Illumina data using scripting to automate the analysis.
In this tutorial you will be introduced to:
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:
This hands-on tutorial will cover installation and use of the SMRT portal at MSI to analyze PacBio sequencing data. The basics of full genome assembly and transcript assembly will be covered. At the end of this tutorial, participants should be able to: