MSI Users Bulletin - June 2021

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

To request technical assistance with your MSI account, please contact the Help Desk via email at, by using the online Support Request Form, or by scheduling a video consultation.

MSI Users pipeline information

1. Agate Update:

Agate will be delivered in mid-August, after which installation and acceptance testing is expected to take eight weeks. At that point it will start full integration with MSI infrastructure, in order to enter production in late fall. We will update the Agate page on the MSI website with up-to-date information as it becomes available.

2. Blackwell Update:

Blackwell, MSI’s new HIPAA-compliant system, is being installed. Third-party compliance review and beta testing are scheduled for July, and we anticipate system acceptance in August.

3. Core Dumps: 

The ability for users to create "core dumps" has been re-enabled; they remain off by default. A core dump is essentially a snapshot of what was in computer memory when a running program was halted by an interrupt. They are mostly used by people who are writing their own code, using these files as input to advanced tools like debuggers. Core dumps can be quite large in size, so if you don’t have a need for them, we recommend you not enable their creation.

Instructions for enabling core dumps can be found on our website.

4. IPA Retirement:

MSI will be discontinuing the license for Qiagen’s Ingenuity Pathway Analysis (IPA) software effective July 29, 2021.

While IPA has historically been a leader in pathway analysis, over the past several years, freely available pathway databases and open-source tools for pathway analysis have become available. These tools rival Qiagen’s IPA and support a broader set of study species. Several of these open-source tools are the preferred approaches for MSI’s analysts. While MSI will no longer offer IPA, we will continue to offer several different resources for pathway analysis.

For the last several years, MSI has reviewed the software licenses we purchase to make sure our software offerings line up with our mission to provide high performance computing (HPC) services. IPA runs on Qiagen’s servers, not our HPC infrastructure, and therefore does not meet our criteria for continuing support. IPA is also one of the most expensive licenses MSI purchases and the cost has been increasing every year. In our current budget climate, MSI can no longer justify this expenditure when there are equally powerful free options available.

The MSI website will be updated with the most current information. The Research Computing website has a list of IPA alternatives.

Questions can be sent to the MSI Help Desk.

5. Summer Tutorials:

The summer tutorial schedule has been posted to the MSI website.  There will be no in-person tutorials this summer, but online options are available. Instructions for participating can be found on the tutorials' webpages.

The initial tutorial, Introduction to MSI, will be held online via Zoom on June 22. 

For the other tutorials, please view the tutorial on the MSI YouTube channel. You can then participate in a live Q&A session with one of the MSI experts on this topic. Links to the tutorials and instructions for participation can be found on their individual webpages.

6. MSI Operations During COVID-19 Pandemic:

MSI staff are continuing to work from home. We plan to begin the transition to having staff on-site during August, and hope to have the Help Desk and SDVL in Walter Library re-opened by the start of the fall semester.

All MSI systems continue to be operational and can be accessed remotely. You can contact the MSI Help Desk for assistance by using the online Support Request Form, requesting a video consultation, or emailing

The MSI labs are closed while MSI staff are not working on campus. We are not processing access requests during this time. 

7. Requesting MSI Resources for COVID-19 Research: 

The conditions surrounding the COVID-19 epidemic are continuing to evolve and MSI staff want to do what we can to support and accelerate research and development that is directed toward this epidemic. If you are engaged in COVID-19 research, please contact us with a synopsis of your research and briefly describe how staff expertise or additional computational and data storage resources can help to advance and accelerate your research. We are working to develop “resource grants” for COVID-19 projects, which might include things like “code/workflow optimization,” “accelerated access to computing,” and “added allocations of storage” for COVID-19 related research. Your feedback will help us figure out how best to proceed. Please email withCOVID-19 Research” in the subject line.

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