Becker Library has partnered with the Center for High Performance Computing (CHPC) and the Institute for Informatics (I2) to offer free trainings to the Washington University Medical Center community on a variety of research computing topics, including:
- Computing 101
These workshops are meant to serve as an introduction to research computing basics and prepare participants for ongoing learning. Check below to see what’s coming up or sign up for the mailing list to be notified each time a new workshop is scheduled.
Introductory R workshops will be coming in September. Sign up for the mailing list to be notified when registration opens.
These workshops were geared toward researchers new to high performance computing and the command line interface. Each workshop started with a 30 minute presentation introducing important background concepts related to computing and then the remaining 90 minutes were devoted to hands-on activities. While these workshops were focused on using the CHPC, the knowledge gained could be applied to other computing environments.
#1 Tools to Connect and Move Data & Getting Around the Linux Command Line Interface – 6/19/18
Goals: to develop a basic understanding of the tools needed to connect to the CHPC and transfer data back and forth, and become familiar with the Unix file system and basic Unix commands
#2 Text Editors and Shell Scripts – 6/26/18
Goals: to gain knowledge of some of the options for text editors and learn how to write and execute basic shell scripts
#3 Running Jobs on the CHPC Cluster – 7/3/18
Goal: to learn how to write and submit batch scripts to run applications on the CHPC cluster
Additional Computing 101 resources: basic Unix commands cheat sheet
Two MATLAB workshops were led by a MathWorks Engineer on Thursday, May 3, 2018. See below for a description of each of the workshops and links to workshop materials.
Session #1: Image processing for medical applications using MATLAB
This MATLAB training seminar presentation included the following topics:
- Analyzing medical images using MATLAB Apps
- Image thresholding
- Finding ROI properties
- Automating your workflow with MATLAB
Workshop slides and other materials can be found here.
Session #2: Parallel Computing with MATLAB
This workshop was hands-on and focused on using MATLAB on the CHPC cluster. The following topics were covered:
- Getting started with parallel computations in MATLAB
- How well does your code scale?
- What’s taking so long? Profiling in parallel
The slides and hands-on activities from this workshop are posted on the CHPC MATLAB page.
These workshops were geared toward researchers new to programming and Python. Each workshop started with a 30 minute presentation covering important background information and then the remaining 90 minutes was devoted to hands-on activities.
Introduction to Python #1 – Getting Started with Python – 7/17/18 and 7/18/18
Goals: to develop a basic understanding of the Python programming language and to learn to run basic Python code in the interactive Python environment, Jupyter Notebook
Introduction to Python #2 – Using Python for Data Analysis – 7/24/18 and 7/25/18
Goals: to learn to write Python code to perform data analysis and visualization and to learn to run Python code in the virtual environment set up on the CHPC
These workshops were geared toward researchers new to programming and R. Each workshop started with a 30-minute presentation covering important background information and then the remaining 90 minutes was devoted to hands-on activities.
Introduction to R #1 – 2/27/18 and 3/1/18
Objectives: introduce R objects and classes, provide an overview of some popular data structures (vectors, matrices, and data frames), and touch on basic ways to manipulate data
Introduction to R #2 – 3/6/18 and 3/8/18
Objectives: introduce basic methods of data visualization, provide an overview of R packages and Bioconductor, and touch on how you go about using R on the CHPC cluster
Introduction to R #3 – 3/20/18 and 3/22/18
Objectives: introduce genomic data analysis using R/Bioconductor and associated visualizations using ggplot2
Additional Introduction to R resources: R Reference Card
Research Computing Team
at Becker Library
at the CHPC
at the Institute for Informatics
Senior Computer Specialist
Center for High Performance Computing