MSI Users Bulletin - December 2025

1. Sizing for Slurm Workflows: MSI has written procedures describing how to determine the amount of resources needed for interactive and batch jobs on MSI systems when migrating or building new workflows. These instructions can be found in the Knowledge Base on the MSI website: Slurm Job Right-sizing. 

2. Software Calendars: MSI provides many software packages to users. The complete library and instructions can be found on the MSI website’s Software page. 

Please note that some software packages have a limited number of licenses available (Abaqus, COMSOL, GraphPad Prism, Imaris, Materials Sudio, Mimics, USEARCH). If you are using one of these, you must reserve time on the appropriate software calendar (software calendars are linked from the Software page). Please note:

• If you are using a software package without a calendar reservation, MSI reserves the right to cancel the session.
• As of December 2025, if a user is found to be using software without a calendar reservation repeatedly (more than once), MSI reserves the right to remove that user’s access rights to that software.

COMSOL is now only available to those who request access. Please contact the Help Desk for access to COMSOL and other limited-license software.

3. Updates to 'bioref' Databases: /common/bioref has new databases and reference directories. For the latest information related to ‘bioref’ please refer to z.umn.edu/bioref

The following are new additions to bioref:

• /common/bioref/kraken2
  • Contains two pre-made metagenomics indices downloaded from the following link: https://benlangmead.github.io/aws-indexes/k2. The suffix indicates the date of release (standard) or release number (silva).
• /common/bioref/microbiome
  • Contains dada2_taxonomy_references (see https://benjjneb.github.io/dada2/training.html for more information) and reference databases from the various biobakery_workflows (see https://huttenhower.sph.harvard.edu/biobakery_workflows/ for more information)
• /common/bioref/cellranger_10x
  • Contains pre-built cellranger genome indices for the gene expression (gex), VDJ (vdj), and ATAC-seq/multiome (arc) 10X genomics library preps for a few different species as well as a combined human and mouse genome index. It also contains the probe set CSV files that are required for human and mouse 10X Flex library demultiplexing.
• /common/bioref/splitpipe_parse
  • Contains pre-built split-pipe indices for human (hg38) and mouse (mm10) genome for demultiplexing single-cell libraries from Parse Biosciences. Indices were built with the system module version of parse-pipeline v1.5.0.

4. Citrix: Tier 1 storage is once again accessible to all our software desktops. We have posted updated documentation for Citrix on our website. A video demo is available on our MSI Youtube Channel.

5. Call for D2D Building Research at the State Fair: The application period is open for the Driven to Discover Research Facility at the 2026 Minnesota State Fair, August 27 - September 7, 2026. The D2D facility allows researchers to reach a large, diverse pool of participants for their studies, while giving fairgoers a fun and easy way to participate in research. If you have a suitable project, please submit your application by January 20, 2026. You can see complete information and the application link at the D2D website. 

6. Primary Storage Migration Project: The migration project of research projects’ storage to our new primary storage vendor, VAST, is essentially complete. Thank you for your support and assistance in getting your data moved. You can see information about this project on the migration webpage.

7. Research Computing Exhibition: Save the date! The 2026 Research Computing Exhibition will be held on Thursday, April 23, 2026, in Coffman Memorial Union. The Exhibition will include judged poster sessions with prizes, as well as presentations, lightning talks, and informational posters from RC units. The Call for Posters for the poster competitions will be sent out on January 31, 2026. The RC Exhibition webpage will be updated as the schedule is developed. 

8. PEARC 2026: The annual conference on Practice and Experience in Advanced Research Computing (PEARC) will be held in Minneapolis next year, July 26 - 30, 2026. The organizers are developing the program and gathering names of those interested in volunteering. You can sign up for the PEARC 26 newsletter and check the PEARC 26 website for the most recent information. 

9. Spring Tutorials and Workshops: MSI and its partners will hold a number of tutorials during the Spring 2026 semester. Links to individual series are below; a consolidated list of courses that will help you hone your research computing skills can be found at the Research Tools and Computing Workshops portal site. 

a. MSI: The MSI Spring 2026 tutorial schedule and registration links can be found on the MSI Tutorials page. MSI’s tutorials are intended to help users achieve the best results using MSI systems. Most tutorials are hybrid, with both in-person and online (Zoom) participation. In-person tutorials are held in room 575 Walter Library. 

Videos of past tutorials and tutorial materials can also be found on the Tutorial Materials and Recordings page. 

b. GEMS Learning: GEMS Learning provides modular, non-credit digital and data-science training for working professionals and students interested in hands-on food, agriculture, and natural resource applications. They are currently offering several asynchronous courses; see the GEMS Learning webpage for course details and registration information. 

c. U-Spatial: U-Spatial offers instructor-led workshops focusing on different geospatial tools and technologies. Their current offerings are posted on the U-Spatial Training page on the U-Spatial website. 

10. Upcoming Research Computing Events:

a. DSAI Hub: Information about upcoming events sponsored by the DSAI Hub, one of MSI’s Research Computing partners, can be found on the DSAI Events webpage. 

b. IIB Lecture Series: The International Institute for Biosensing (IIB), one of MSI’s Research Computing Partners, hosts a Precision Sensing Lecture Series featuring experts. Most lectures are held in person, with lunch provided. See the IIB Lecture Series webpage for the schedule. 

c. U-Spatial Mapping Prizes: Information about the 2026 Mapping Prizes will be posted on the Spatial University website when the schedule is finalized.

11. MSI Operations: MSI staff work under a hybrid model; not all staff work on-site full time. All MSI systems can be accessed remotely. 

The Help Desk, located at 587 Walter Library on the East Bank campus, provides assistance to users for all issues related to using MSI resources. The Help Desk is staffed Monday through Friday:

• 9 a.m. - 12 p.m.
• 1 - 4 p.m.

Follow the contact instructions found on the Help Desk webpage to request assistance. 

12. Useful Webpages: Looking for help with using MSI or other RC resources? One of these pages may have the information you need:

• Our Services
• Our Resources
• Getting Started at MSI (includes Quickstart Guides)
• MSI Systems Status
• Software at MSI
• MSI Help
• Tutorials
• Knowledge Base
• Staff Listing and Areas of Expertise
• Proposal Support
• Upcoming Events 

MSI partners:

• Research Computing website
• Data Science and AI Hub website
• International Institute for Biosensing website
• U-Spatial website
• GeoCommunities