MSI Users Bulletin - June 2023
The Users Bulletin provides a summary of new policies, procedures, and events of interest to MSI users. It is published quarterly.
1. SSH Host Key Fingerprints Change:
As a routine security measure, as of June 7, SSH host keys used to secure all login servers for Mesabi/Mangi and Agate have been changed. This change only impacts SSH connections (including ssh, scp, and sftp) to MSI’s login servers.
The MSI website has instructions, with short video illustrations, about how to update your SSH client with the new host key fingerprints.
2. dbGaP on Tier 1
MSI is now able to support analysis of dbGaP data on its main systems in secure project spaces. To request a project space for dbGaP analysis, please contact the Helpdesk for further details and to start the process with our team.
3. bioref
MSI’s biological sequencing reference databases risdb (/panfs/roc/risdb) and risdb_new (/panfs/roc/risdb_new), are being replaced by bioref (/common/bioref/) effective immediately. Risdb and risdb_new will continue to be accessible until MSI’s September Maintenance Day (9/6/23). bioref is a directory on our system that houses the latest releases of 34 NCBI BLAST databases and 2,411 ENSEMBL eukaryotic species genome sequences (FASTA) and gene annotations (GFF and GTF formats), along with their pre-built genome indices that can be used with read alignment software such as BWA, Bowtie, Bowtie2, and HISAT2. BLAST nucleotide database indices are also available for each genome.
To find out more about the contents and organization of files within bioref, please see the bioref page on the website.
4. Single Cell Symposium 2023
The U of M Genomics Center and MSI are hosting a Single Cell Symposium on Thursday, June 22, 8:30 a.m. – 12:30 p.m., in 402 Walter Library. The symposium will feature in-depth presentations from U of M experts in immunology and the biology of aging, as well as an open panel discussion to talk about single-cell challenges, techniques, and best practices in this evolving field. Complete information and registration can be found on the UMGC website.
5. Research Computing Collaboration and Coffee
Research Computing Collaboration and Coffee events will be held on July 19 and August 16, both at 2:30 – 3:30 p.m., in 401 Walter Library. RC users are welcome to join staff members for informal discussions and treats.
6. Summer Tutorials, Workshops, and Seminars
a. MSI: MSI’s tutorials are intended to help users achieve the best results using MSI systems. The Summer 2023 schedule is:
Intro to MSI: Tuesday, July 11, 1-2
Intro to Linux: Wednesday, July 12, 10 – 3
Job Submission and Scheduling at MSI: Tuesday, July 18, 1 – 3
Interactive Computing at MSI: Thursday, July 20, 1 – 3
Introduction to Compiling and Profiling at MSI: Tuesday, July 25, 1 – 3
Programming With Python: Tuesday, August 1, 10 – 3
Advanced Python: Thursday, August 3, 10 – 3
Tutorials are hybrid, with both in-person and online (Zoom) participation. In-person tutorials are held at MSI in Walter Library. Descriptions and registration links are posted on the MSI Events page and the MSI Tutorial Calendar.
Past tutorials can be viewed on the MSI YouTube channel.
b. Characterization Facility: The Characterization Facility is holding a series of seminars to foster interaction between users and staff scientists: CharFac's summer series. An informatics-related seminar is part of the series:
CharFac's advanced data analysis capabilities. Presented by Dr. Guichan Yu, MSI Informatics and Computing group. August 16, 11 a.m. - 12 p.m., room 212, Civil Engineering Building.
7. Call for Papers – IEEE HPEC 2023
The IEEE’s High Performance Extreme Computing 2023 Virtual Conference (25 – 29 September) is accepting papers through July 7. Papers should clearly describe advances in high performance extreme computing technologies. The complete Call for Papers can be found on the conference website.
They are accepting both full papers (up to six pages not including references) and extended abstracts (up to two pages including references). Accepted papers will be notified on August 15, and camera-ready final papers will be due by August 31.
8. 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
9. Useful Webpages
Looking for help with using MSI? One of these pages may have the information you need: