National Computational Science Institute Logo


Last year, I attended a two-and-a-half-day community and curriculum building workshop. It could not have been more perfectly timed. I was able to come up with a solid plan for my CMSE401 parallel programming course which I ended up teaching this last spring.

This year I was not able to attend the workshop in Tulsa OK (darn jury duty!):

link to CBHPCCD19

However, I did arrange with the organizer (Aaron Weeden) and was able to give a video conference presentation about my class. Hopefully this year's participants found my talk useful. Here is a link to my slides in case anyone is intertested:

Link to Slides

Do More, Faster: Utilizing Advanced Computational Resources in Your Research Team

Tue 21 May 2019 by Dr. Dirk Colbry

INSciTS Logo

Here are my slides from the SciTS conference last month.

The SciTS conference is the annual international forum dedicated to SciTS, bringing together thought leaders from a broad range of disciplines and fields, including: communications, management, social and behavioral sciences, information technology, systems science, and translational research. It provides investigators …

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Automating Scientific Image Analysis Workflows

Tue 23 April 2019 by Dr. Dirk Colbry

GA Title Slide

I was asked to give a talk to Michael Murillo machine learning seminar group. Michael put the group together as a first step to gather topics/ideas for a graduate level machine learning class that CMSE will be teaching in the fall.

In this talk I introduced a difficult machine …

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Extracting Desire to learn (D2L) zip files into student folders

Mon 15 April 2019 by Dr. Dirk Colbry

D2L Logo

At MSU we use Desire to Learn for our classroom content management system. Students can go to D2L to get their assignments and turn in their assignments though the D2L dropbox.

When grading, I can download all of the student's submissions into a zip file such as the following:

Part …

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Accessibility of Jupyter for Impaired Individuals

Fri 05 April 2019 by Dr. Dirk Colbry

Asha in front of her poster

This poster presents work by CMSETech Intern, Ahsa Shekar and her work on finding ways to make Jupyter More accessible.


Jupyter is an open-source programming environment that uses "literate programming" by combining documentation, coding and visualization into one file format. The Jupyter notebook format is also particularly well-suited for …

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The challenges of developing research tools in active and responsive open source communities

Fri 05 April 2019 by Dr. Dirk Colbry

Poster with Ty and Hattie

This poster presents work by Professorial Assistance, Ty Buckly and Hattie Pimentel and their work on building an image annotation system inside of Jupyter.


Scientists often gather observations of the world using images and need efficient image annotating tools to extract data from these images. Project Insight seeks to …

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HPCC SLURM Buy-in Notes

Thu 28 March 2019 by Dr. Dirk Colbry


This year, the HPCC moved over to SLURM. Overall, I think the new scheduler is nice but it required me to relearn a bunch of things I have gotten to know by reflex.

One nice new feature is that I can manage our own Buy-in account. The CMSE department has …

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Understanding Research Technology Support and Where it Fails

Tue 26 March 2019 by Dr. Dirk Colbry

Image of a Microscope

I was invited to give a talk to a newly formed IT Research Support group here on MSU campus. As the name suggests, the purpose of this group is to find the best ways to help researchers use technology to do their science.

This talk was a patchwork of many …

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Managing Files on the MSU Engineering Jupyterhub server

Fri 08 March 2019 by Dr. Dirk Colbry

Disk Icon

The MSU Engineering Jupyterhub server provides 2GB of disk storage space for each student. It can be helpful to learn some disk management so you can use this space effectively.

For example, pip install uses a temporary folder when downloading packages. Periodically, deleting this folder can significantly free up space …

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Virtual Reality Talk at the MSU Library

Tue 26 February 2019 by Dr. Dirk Colbry

VR Image

A few weeks ago I was asked by Terence O'Neill to give a talk to the VR/AR seminar group being held at the library. He wanted me to talk about our "Mobile beast" and show how we are using VR equipment in CMSE.

The VR equipment had a bug …

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