Research Computing

Becker Library offers free trainings to the Washington University Medical Center community on a variety of research computing topics, including:

  • Computing Basics
  • MATLAB
  • Python
  • R

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.

Sign up for the mailing list

Contact Maze Ndukum (ndukummaze@wustl.edu) or Marcy Vana (vanam@wustl.edu) with any questions.

Upcoming Workshops

There are no scheduled workshops at this time.

View a comprehensive list of Library classes and workshops

Previous Workshops

These virtual computing basics workshops were offered in collaboration with Research Infrastructure Services (RIS)​ and the Institute for Informatics (I2), and designed for those without any prior experience using the Unix Command Line Interface (CLI) and High Performance Computing (HPC).  All workshop materials can be found here.

The Unix Shell and Command Line Basics​ – 9/7/2021

This workshop introduced the Unix command line interface, the Unix file system, and basic Unix commands. Attendees learned how to create, explore and manage Unix folders and files.

Software Applications Needed to Work in HPC Environments – 9/14/2021

This workshop introduced text editors, shell and batch scripts, Docker container technology, and the ssh protocol. Attendees learned how to write, edit and run shell scripts, how to create a simple Docker container, and how to connect to RIS Scientific Compute Platform.

Basics of Submitting Jobs/Tasks to RIS Scientific Compute Platform  – 9/21/2021

This workshop introduced basic commands for submitting jobs to RIS Scientific Compute Platform’s queuing system. Attendees learned to use Docker and queuing system commands to submit jobs in both interactive and non-interactive modes.

Single-Cell RNA-Sequencing (scRNA-Seq) Data Analysis Using R and RIS Compute Platform – 9/28/2021

This workshop discussed analyses of scRNA-Seq data using R on the RIS Scientific Compute Platform. Attendees learned how to create and use a Docker container image for scRNA-Seq data analysis to submit a job that sets up RStudio on the RIS Scientific Compute Platform. Finally, R packages were used to explore and visualize the data.

These MATLAB webinars were organized in collaboration with WUIT’s Research Infrastructure Services (RIS), and were led by MathWorks Engineers. See below for a description of each workshop and links to the workshop materials.

 Parallel Computing with MATLAB – 3/25/2021 at 10AM

Using the Parallel Computing capabilities in MATLAB allows users to take advantage of additional hardware resources that may be available either locally on their desktop or on clusters, clouds, and grids. By using more hardware, you can reduce the cycle time for your workflow and solve computationally and data-intensive problems faster.  This webinar discussed a range of workflows available to scale MATLAB applications with minimal changes to your MATLAB code and without needing to learn low-level programming. Below are some of the highlights discussed:

  • Leveraging multiple cores or CPUs
  • Working with high-level constructs—parallel for-loops, special array types, and parallelized numerical algorithms.
  • Scaling up to utilize clusters, grids, and clouds
  • Utilizing tall and distributed arrays to work with large data sets
  • Using MATLAB for GPU computing

 NOTE: MATLAB is accessible on WUIT’s RIS compute cluster. You can request access to RIS compute and storage to leverage MATLAB, to do so, use your WUSTL key to log in here (All WashU Faculty have access to 5TB of free storage available to them). Please visit the RIS website to learn more.

Workshop recording and other materials are located here.

Image Processing Made Easy Using MATLAB – 3/25/2021 at 1PM

Image processing is the foundation for building vision-based systems based on cameras and frame grabbers. You might have a new idea for using your camera in the fields of engineering, sciences, biomedical, or oceanography, for example, and are not sure where to start. This webinar focussed on several key workflows to make things easy and help get you started. The real-world examples presented were focused on:

  • Pre-processing images using enhancement and filtering techniques
  • Separating objects of interest using segmentation techniques
  • Testing your algorithm on large sets of images

Some highlights discussed during the webinar include:

  • MATLAB help documentation and examples help with getting started quickly
  • Interactive apps and live scripts enable exploration of different techniques
  • Extensive library of built-in image processing algorithms

Workshop recording and other materials are located here.

 

Using Python for Basic Data Visualization – March 2021

This workshop introduced three popular libraries used for data visualization in Python. Attendees learned how to create and customize simple Python plots using the Matplotlib, Seaborn, and Plotly Express libraries. Workshop materials and a recording of the workshop can be found here.

Using Python for Basic Data Exploration and Manipulation – February 2021

This workshop introduced the Python programming language. A practice dataset was used to demonstrate import, exploration & manipulation of data from a dataframe using the Pandas library. Workshop materials and a recording of the workshop can be found here.

Basic Data Analysis Using Python – February 2021

This Love Data Week workshop introduced popular libraries for data analysis in Python and demonstrated common data analysis tasks including data import, exploration & manipulation using the Pandas library as well as data visualization using the Matplotlib, Seaborn, and Plotly Express libraries. The hands-on exercises were presented in Jupyter Notebook. All the workshop materials can be found here.

R vs. Python – Love Them Both? – October 2020

This workshop was offered by WashU’s Institute for Informatics, University Libraries and Becker Medical Library on Zoom. The workshop introduced some common data analysis tasks in the R and Python programming languages and explored which language is better suited for a particular task. During the hands-on portion of the workshop, basic Python and R code were explained using the interactive web-based environments, repl.it and RStudio Cloud respectively. The workshop materials are located here.

 

R Workshops

These virtual workshops were geared toward researchers new to programming and R. During each session important background concepts were introduced in a simple presentation format, followed by hands-on exercises. The workshop materials can be found here.

Introduction to R – 10/12/2021

This workshop introduced R data objects and functions, basic data exploration, manipulation, and visualization, all using R base.

Introduction R – Data Visualization in R Using ggplot2 – 10/19/2021

This workshop introduced R packages and covered installing, loading and managing R packages as well as basic data visualization using the ggplot2 package.

Introduction to R – Bioconductor – 10/26/2021

This workshop introduced Bioconductor and covered installing, loading and managing Bioconductor packages as well as basic genomic data exploration with the VariantAnnotation package.

Visualization of COVID-19 Data Using R – 11/2/2021

This workshop was led by a Bioinformatics Scientist from the Institute for Informatics (I2), and explores the structure of publicly available COVID-19 data and methods to visualize the data with an aim to understand disease epidemiology. The R code for this session can be found in this RStudio Cloud Project. All workshop materials are located here.

R vs. Python – Love Them Both? – October 2020

This workshop was offered by WashU’s Institute for Informatics, University Libraries and Becker Medical Library on Zoom. The workshop introduced some common data analysis tasks in the R and Python programming languages and explored which language is better suited for a particular task. During the hands-on portion of the workshop, basic Python and R code were explained using the interactive web-based environments, repl.it and RStudio Cloud respectively. The workshop materials are located here.

Genomic Data Analysis Using Bioconductor – October 2020

This workshop was offered by WashU’s Institute for Informatics, University Libraries and Becker Medical Library on Zoom. This virtual workshop provided an introduction to using R and Bioconductor for computational genomics. EdgeR and ShortRead packages were used to perform RNA sequencing data analysis, introducing various data formats, data input and output, data analysis and visualization. During the hands-on activities, R code was explained using the interactive web-based environment, RStudio Cloud. The workshop materials are located here.