MSI Users Bulletin - September 2022

The Users Bulletin provides a summary of new policies, procedures, and events of interest to MSI users. It is published quarterly.

1. MSI Operations: MSI staff are now working under a hybrid model; not all staff are working on-site full time. All MSI systems are operational and can be accessed remotely.

To request technical assistance with your MSI account, contact the Helpdesk:

2. Annual Renewals: The annual renewal period will open on November 1, 2022. MSI will notify PIs and Group Administrators when the renewal forms are available on our website. Renewals should be submitted by November 30. Non-renewed accounts will be closed at the end of the calendar year. Please contact Becky von Dissen (vondi001@umn.edu) if you have any questions.

3. Blackwell Update: Blackwell is a new HPC cluster that is designed to support data that are protected by HIPAA. The Blackwell team is working hard to address the University's requirements for a system to host Patient Health Information (PHI). We anticipate being ready to put Blackwell into production in October. If you use data protected by HIPAA and anticipate needing to use Blackwell, please let us know by sending a message to help@msi.umn.edu.

4. Fall Tutorials and Workshops: Fall schedules for several tutorial and workshop series related to research computing have been announced. They include MSI’s fall tutorial series, the Software Carpentry series, Data Management Bootcamps, and workshops from U-Spatial.

a. MSI Tutorials: MSI’s tutorials are intended to help users achieve the best results using MSI systems. The Fall 2022 tutorials will be hybrid, with both in-person and online (Zoom) participation. All tutorials are held in the Scientific Development and Visualization Lab, room 575 Walter Library. Descriptions and registration links can be found using the MSI Events page. Past tutorials can be viewed on the MSI YouTube channel.

  • Intro to MSI
    • Thursday, September 29, 1 – 2 p.m.
  • Intro to Linux
    • Tuesday, October 4, 1 – 4 p.m.
  • Job Submission and Scheduling at MSI
    • Thursday, October 6, 1 – 3 p.m.
  • Interactive Computing at MSI
    • Tuesday, October 11, 1 – 3 p.m.
  • Programming With Python
    • Thursday, October 13, 10 a.m. – 3 p.m.
  • Data Storage Systems and Data Analysis Workflows
    • Wednesday, October 19, 1 – 3 p.m.
  • Advanced Python
    • Thursday, October 27, 10 a.m. – 3 p.m.
  • Software Management at MSI
    • Tuesday, November 1, 1 – 3 p.m.
  • RNA-seq Analysis
    • Tuesday, November 8, 1 – 3 p.m.
  • Parallel Computing on Agate
    • Wednesday, November 9, 1 – 3 p.m.
  • Intro to Single-Cell Genomics
    • Monday, November 14, 1 – 4 p.m.
  • Intro to Compiling and Profiling at MSI
    • Thursday, November 17, 1 – 3 p.m.

b. Software Carpentry: Software Carpentry workshops are hands-on events that cover core computational research skills to be productive as an individual scientist or in small research teams. These workshops offer graduate students, staff, and faculty practical exercises on basic computational research skills. No previous experience is needed and each workshop is taught by experienced researchers who use these tools in their own work. This is an excellent opportunity to learn about tools that will help your research process become more efficient, rigorous, and reproducible. Descriptions of Software Carpentry classes and links for registration can be found on the DASH website. Some classes will be held online, others are in person; check the individual descriptions.

  • Databases and SQL (in-person)
    • Monday and Wednesday, September 19 and 21, 10 a.m. – 12:30 p.m.
    • 575 Walter Library (Scientific Development and Visualization Lab, MSI)
  • Version Control With Git (in-person)
    • Tuesday, September 27, 1 - 4 p.m.
    • 575 Walter Library (Scientific Development and Visualization Lab, MSI)
  • Plotting and Programming in Python (in-person)
    • Wednesday, Thursday, and Friday, September 28 – 30, 1 – 3:30 p.m.
    • 5-130 Phillips-Wangensteen Building (Data Visualization Lab, Health Sciences Library)
  • R for Reproducible Scientific Analysis (online)
    • Tuesday, Wednesday, and Thursday, October 4 - 6, 1 – 4 p.m.
  • Introduction to LaTeX (in-person)
    • Monday, October 24, 1 – 2:30 p.m.
    • 575 Walter Library (Scientific Development and Visualization Lab, MSI)

c. Data Management Bootcamp: The Data Management Bootcamp is a series of workshops to build and enhance your data management strategies. Topics range from introductory skills to specific tool-based workshops on citation managers, backup workflows, writing your dissertation with R, and publishing your data. Sign up for a single workshop or for the entire series. Workshops will be held online via Zoom. Free to U of M graduate students. The description of the series and registration links can be found on the U of M Libraries website.

  • Tools for Organizing PDFs and Article Citations
    • Monday, September 19, 10 a.m. – 12 p.m.
  • Storage, Back-up, and Versioning, Oh My!
    • Monday, October 3, 10 a.m. – 12 p.m.
  • Writing Your Thesis or Dissertation With R Markdown, GitHub, and Friends
    • Monday, October 24, 10 a.m. – 12 p.m.
  • Publishing (With) Data
    • Monday, November 14, 10 a.m. – 12 p.m.

d. U-Spatial Workshops: U-Spatial offers a variety of instructor-led workshops focusing on different geospatial tools and technologies. These workshops are offered at a minimal cost to U of M students, faculty, and staff. The Fall 2022 schedule can be found on the U-Spatial website.

5. UMII-MnDRIVE PhD Graduate Student Assistantships: The application period for the 2023 UMII-MnDRIVE PhD Graduate Assistantship Program is open. This program supports U of M PhD candidates pursuing research at the intersection of informatics and any of the five MnDRIVE areas: Robotics, Sensors and Advanced Manufacturing; Global Food Ventures; Advancing Industry, Conserving Our Environment; Discoveries and Treatments for Brain Conditions; and Cancer Clinical Trials.

PhD candidates are eligible to apply. Graduate students are expected to have successfully completed their preliminary oral exam by the start of the appointment. The application deadline is October 4, at 5:00 pm CDT. To submit an application and see complete program information, visit the MnDRIVE-UMII Informatics PhD Graduate Assistantship Program URL on the UMII Research Funding Portal. Log in with your U of M credentials (preferred) by selecting “UMN Login” from the Login dropdown, or create a SM Apply account to access the application. 

6. Jobs Available at MSI:

7. Useful Webpages: Looking for help with using MSI? One of these pages may have the information you need: