MSI Users Bulletin - September 2023

1. Annual Renewals

The annual renewal period will open on November 1, 2023. 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.

2. Graduate Assistantships

The application period for the 2024 DSI-MnDRIVE PhD Graduate Assistantship Program is open. This program supports U of M PhD candidates pursuing research at the intersection of data science and any of the five MnDRIVE areas: Robotics; Global Food; Environment; Brain Conditions; and Cancer Clinical Trials. The deadline for applications is Friday, October 6, 2023 at 5 p.m. CDT. Complete information and application link.

3. Seed Grants

The Research Computing Seed Grant program is now the DSI Seed Grant Program. DSI Seed Grants are intended to promote, catalyze, accelerate, and advance U of M-based data science research so that U of M faculty and staff are well prepared to compete for longer-term external funding opportunities.

Proposals from all disciplines and across all campuses, including interdisciplinary collaborations, intersecting with data science are encouraged to apply, with priority given to proposals that will enable or bridge applications to larger funding opportunities and/or create new cross-disciplinary or cross-systems collaborations. Priority will be given to proposals that align with at least one of the areas of the MnDRIVE initiative and the current DSI focus areas.

Complete information, including application instructions and deadlines, can be found at the following links:

• RC Funding Opportunities overview
• DSI Small Seed Grants (up to $10,000); awarded quarterly, next deadline October 6, 2023
• DSI Medium ($10,000 - $50,000) / Large ($50,000 - $120,000) Seed Grants; awarded annually, next deadline October 6, 2023

4. Bioref

MSI’s biological sequencing reference databases risdb (/panfs/roc/risdb) and risdb_new (/panfs/roc/risdb_new) have been replaced by bioref (/common/bioref/). bioref houses quarterly releases of 34 NCBI BLAST databases and yearly releases of 2,411 eukaryotic genomes from Ensembl. The genome data includes the reference assembly (FASTA), gene annotations (GFF/GTF), BWA index, Bowtie index, Bowtie2 index, HISAT2 index, and nucleotide BLAST database. 

New BLAST database folder location for the latest release: /common/bioref/blast/latest

• BLAST databases within bioref will be updated quarterly on MSI maintenance day (first Wednesday of the month) in January, April, July, and October.

New Ensembl database folder location: /common/bioref/ensembl

• Ensembl databases will be updated once a year on MSI maintenance day in January.

All bioref database updates will be kept on the MSI systems for four years.

To find out more about the contents and organization of files within bioref, please see the bioref page on the website.

5. Informatics Interest Group

Informatics Interest Group is a Google group sponsored by MSI that is open to all bioinformatics and computational biology researchers. The focus of the group is to publicize new software and sources of interest, to highlight local seminars and events relevant to this community, and to be a place for discussion. The group meets every other Wednesday, 3:30 – 4:30 p.m., in 101 Walter Library and on Zoom. Complete information, including a link to join the group, can be found on the UMGC webpage.

6. Research Computing Collaboration and Coffee

Research Computing Collaboration and Coffee events will be held on October 18 and November 15, at 2:30 – 3:30 p.m., in 501 Walter Library. RC users are welcome to join staff members for informal discussions. Due to changes to the U’s food and beverage policy post-COVID, as described in Jim Wilgenbusch’s email of August 14, you’ll now need to bring your own beverage and/or snack. if you’re so moved, you’re welcome to bring a treat to share (many thanks to the people who did this at the August gathering).

7. 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, training from U-Spatial and GEMS Learning, the Software Carpentry series, and Data Management workshops.

a. MSI Tutorials: MSI’s tutorials are intended to help users achieve the best results using MSI systems. The Fall 2023 tutorials will be hybrid, with both in-person and online (Zoom) participation. All tutorials are held in room 575 Walter Library. The descriptions and registration links will be posted on the MSI Events page and the Tutorial Calendar shortly, when the schedule is finalized.

Past tutorials can be viewed on the MSI YouTube channel.

b. 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 schedule for Fall 2023 can be found on the U-Spatial website.

c. 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. These courses give students practical knowledge to tackle data-science challenges across the agri-food sciences. Current U of M staff, faculty, and students can enroll for free. See the GEMS Learning webpage for course details and registration information.

d. 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 at the Software Carpentry course list. Some classes will be held online, others are in person; check the individual descriptions.

d. Data Management Workshops: The Data Management Workshop Series is designed to help you 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.

8. Upcoming Events of Interest

a. GenoFest 2023: MSI will be participating in GenoFest, the annual conference hosted by the University of Minnesota Genomics Center. The event will be held on Friday, October 6, 9 a.m. – 1 p.m. See more information on the UMGC website.

b. HPEC Virtual Conference: The IEEE High Performance Extreme Computing (HPEC) free virtual conference, organized by MIT in cooperation with SIAM, is the largest computing conference in New England with 125+ talks (30+ AI talks). It will be held September 25 - 29. Complete information and the registration form can be found on the conference website.

c. UMN Spatial Forum 2023: The annual Spatial Forum is sponsored by U-Spatial, MSI's Research Computing partner organization. This event highlights spatial research, teaching, and outreach at the University of Minnesota. It is free and open to the public and features lighting talks, exhibitor booths, and the Borchert Lecture. It will be held November 15 in the Research Collaboration Studio at the O. Meredith Wilson Library. The Borchert Lecture will be presented by Dr. Nadine Alameh, Inaugural Executive Director of the Taylor Geospatial Institute. Register at the event webpage.

9. U-Spatial Mapping Prizes

The winners of the 2023 U-Spatial Mapping Prizes were announced in July, and the winning maps are shown on the Spatial University website.

The deadline for the 2024 competition is May 10, 2024. U of M students from all University system campuses are encouraged to submit their maps. Winners receive cash awards. The Spatial University link above has a link to submission information.

10. 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:

• In-person walk-ins: Monday, Wednesday, and Friday, 9 a.m. - 4 p.m.; 587 Walter Library
• Zoom walk-ins: Tuesday and Thursday, 9 - 11 a.m. and 1 - 3 p.m.; go to Helpdesk Zoom room
• Email: help@msi.umn.edu
• Phone: 612-626-0802
• Online Support Request Form
• Video consultation