Research Computing

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
  • 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.

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Upcoming Workshops

Computing 101

These workshops are geared toward researchers new to high performance computing and the command line interface. Each workshop starts with a 30 minute presentation introducing important background concepts related to computing and then the remaining 90 minutes are devoted to hands-on activities. While these workshops are focused on using the CHPC, the knowledge gained could be applied to other computing environments.

Registration is required for all Computing 101 workshops. Click the workshop titles below to register.

#1 Tools to Connect and Move Data & Getting Around the Linux Command Line Interface – 10/24/18

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

Workshop slides and hands-on activities from the 6/19/18 workshop

#2 Text Editors and Shell Scripts – 11/1/18

Goals: to gain knowledge of some of the options for text editors and learn how to write and execute basic shell scripts

Workshop slides and hands-on activities from the 6/26/18 workshop

#3 Running Jobs on the CHPC Cluster – 11/8/18

Goal: to learn how to write and submit batch scripts to run applications on the CHPC cluster

Workshop slides and hands-on activities from the 7/3/18 workshop

Additional Computing 101 resources: basic Unix commands cheat sheet

Previous Workshops


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

Previous workshop slides and hands-on activities

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

Previous workshop slides, hands-on activities, and data (weather_data_newyork, snow_data)

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 were devoted to hands-on activities.

Introduction to R #1 – 9/6/18 and 9/7/18

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

Slides, hands-on-activities, and data (study data)

Introduction to R #2 – 9/13/18 and 9/14/18

Objectives: introduce basic methods of data visualization using R base and ggplot2

Slides, hands-on-activities, and data (study data)

Introduction to R #3 – 9/20/18 and 9/21/18

Objectives: introduce advanced visualizations using the ggplot2 package in R

Slides, hands-on-activities, and data (nsclc_pd1_msk_2018_clinical_data)

Introduction to R #4 – 9/27/18 and 9/28/18

Objectives: introduce genomic data analysis using R/Bioconductor and associated visualizations

Slides, hands-on-activities, and data (example, counts)

Research Computing Team

at Becker Library

at the CHPC

at the Institute for Informatics

Maze Ndonwi
Maze Ndonwi
Senior Support Scientist
Becker Medical Library

ndonwimaze@wustl.edu

Marcy Vana
Marcy Vana
Senior Support Scientist
Becker Medical Library

vanam@wustl.edu

Malcolm Tobias
Malcolm Tobias
Instructor
Center for High Performance Computing

mtobias@wustl.edu

Xing Huang
Xing Huang
Senior Computer Specialist
Center for High Performance Computing

x.huang@wustl.edu

Aditi Gupta
Aditi Gupta
Post-Doctoral Fellow
Institute for Informatics

agupta24@wustl.edu

Madhurima Kaushal
Madhurima Kaushal
Bioinformaticist
Institute for Informatics

kaushalm@wustl.edu