|O2 for Orchestra Users||12/06/2017||3-5p||Countway 403||User Training Github||Register Here|
|O2 for New Users||12/13/2017||3-5p||Countway 403||User Training Github||Register Here|
|R/Biostatistics||12/12,13,14/2017||1-3p||TMEC L-008/Coutway 403/TMEC 333||Register Here |
O2 for Orchestra Users
O2 for Orchestra Users is designed for those already familiar with the Orchestra LSF job scheduler, or have used other HPC environments. The expectation is that users are already comfortable with linux and submitting jobs, and are ready to convert existing workflows and begin new ones on the O2 slurm compute environment. The lecture portion of this class is one hour, the second hour will be spent clinic-style with HMS RC staff to address workflow-specific questions and help convert commands.
O2 for New Users
O2 for New Users addresses the needs of users who have very little linux experience, and are just getting started with HPC. More time will be devoted to covering linux basics, and the concepts of schedulers and jobs, and data management best practices. No time converting from LSF to slurm syntax will be necessary.
Intro to Python
Python is a popular scripting language for scientific computing and available across all computer platforms. The course will introduce you to some of the basics of the Python language as well as some of the nuances involved with its use specific to the O2 environment. The goal is to provide users with a foundational level of familiarity. Topics covered include basic data types and declaration, flow control (if/else), loops, a brief introduction to constructing a script, and a briefer introduction to modules. The course will be taught on O2, but general concepts are easily translatable to desktop and local installations.
Intro to R/Bioconductor
Intro to using R and Bioconductor. R is a powerful, open-source, highly adaptable statistical language useful for crunching numbers to datasets like those produced by next-gen sequencing. This class covers R basics and learning to think like/understand R. Users will learn how to set up personal R libraries on O2, and use O2 R for its high memory allocations and parallelization. Topics include how to install packages, learn about variables, data types. data manipulation, flow control, and functions, perform simple statistical tests, and create a variety of plots. Laptops are encouraged.
Intro to MATLAB
Matlab has become the “language of science” in the past few decades. It is simple to use, yet powerful enough to be productive on large computing infrastructures. If you need: 1) Fast prototyping of research ideas; or 2) avoid spending too much time in coding instead of doing real science by taking advantage of Matlab’s built-in functions; 3) User friendly graphical interface and educational documentation; 4) Simplicity of code; 5) Easy access to GPU computing power; 6) Easy plotting and presentation of data; you will find this introduction course useful. This course will introduce the basics of the MATLAB coding language with O2-scalability and data presentation.
Intro to Parallel Computing
This is a short introduction to Parallel Computing that will include an overview of the basic concepts of parallel programming: from running your job in an embarrassingly parallel way to writing simple shared and distributed memory parallelization codes in different languages. The seminar will cover several examples of actual parallel codes however it will not have any "hands on" components. A basic programming experience (of any language, no parallelization) is preferred in order to better follow the topics presented during the seminar.
Intro to Perl
Perl is an open source programming language that's flexible, available for nearly all platforms, and is easy to learn. It is well suited for data munging, and processing biological data. Topics covered include variables (scalars, arrays and hashes), numerical and string functions, loops and conditions, regular expressions, and reading and writing files. A brief introduction will be given for subroutines and BioPerl. The class will be focused on running Perl on the O2 cluster, though the fundamentals are applicable for using Perl installations elsewhere.
Intro to Git and GitHub
This course introduces Git and GitHub and covers topics including: Getting Started with Git for version control, Using GitHub Desktop effectively, Collaborating with others on GitHub, and Utilizing GitHub Flow for better workflow. No previous exposure is assumed. We hope attendees will leave the class with the knowledge and tools necessary to start integrating Git into their workflows and excited to begin collaborating on GitHub.
R/Biostatistics is a three-part course covering the basics of RNA-seq analysis with R. This biostatistics course covers standard supervised approaches and functional enrichment analyses of a breast cancer RNA-seq dataset. Topics include edgeR for differential analysis, GOSeq for functional enrichment analyses, and KEGG pathway analysis. High-throughput data visualization techniques are be emphasized. Each class includes a lecture and R practicum, and registration is for all 3 courses. Laptops are encouraged.