PMACS Penn Medicine Academic Computing Services

PMACS NewsletterSpring 2024

May 21, 2024

Leadership Thoughts

Meredith FettersSpring represents a time of new growth and renewal; the common saying is that “April showers bring May flowers”. In this time of new growth, it's an excellent time to highlight some of the department’s new development efforts. Douglas Brunk, PSOM Administration Project Director, has been working diligently with PSOM Administration to tackle the challenging problem of primary investigator fund management and reporting by providing a dashboard view into the status of grant funds, including financial and other status information. Doug has assembled a design and development team made up of Senior Business Administrators, the Office of Research Support Services, and Decision Support. The team has launched a multi-stage project currently focused on grant fund reporting, personnel summaries, and capturing additional encumbrances unavailable elsewhere. Future stages will introduce more features for clinical trials, reporting on other types of funds, effort planning, and advanced modeling.

Also in development are automated Research IT billing processes to provide automated reports and views into PMACS service agreements and tracking the usage rates for better visibility on spending. Work is underway to upgrade to FADS 2.0. The FADS project expects to deliver enhanced reporting for faculty and staff and provide new self-service capabilities for faculty to see and review their data.

Finally, this spring PMACS will be launching an effort with ISC to clean up primary email addresses in PennBox. If you receive a notification about changing your primary email address, please follow up as this will affect your ability to login to PennBox.

 – Meredith Fetters - ACIO Research Information Systems

Staff Spotlight

Announcing Byron Parry's Promotion to Senior Product Owner Manager

Byron ParryByron Parry has recently been promoted to the position of Senior Product Owner Manager within the PMACS Application Development team. In this new capacity, he will assume administrative oversight of the Product Owner team and will directly report to Ginny Barry, Senior Director of Application Development.

Having initially joined the team in 2019 as a Senior Product Owner, Byron made an impact through his contributions in wireframe design and report automation. His responsibilities have focused on clients such as Genetics, the Office of Research Support Services, and PSOM Finance, where he has been the main point of contact. With over 10 years of experience in project and product management, Byron has consistently demonstrated his ability to adeptly handle intricate development projects while fostering positive client relationships.

Byron's academic background includes a Bachelor of Science degree in Information Science & Technology from Penn State, complemented by certifications as a Scrum Leader and Scrum Product Owner. Outside of his professional endeavors, he finds joy in engaging in activities such as golfing, paddleboarding, hiking, and embarking on snorkeling adventures alongside his wife.

Announcing Brian Korn's Promotion to Service Information Officer (SIO)

Brian KornBrian Korn has been promoted to the role of Service Information Officer (SIO) within PMACS Research. Brian joined Penn Medicine Academic Computing Services (PMACS) in 2011 as a Local Support Provider (LSP) providing support to PSOM clients with an emphasis on excellent customer service. In 2015, he was promoted to a Support Supervisor. In this role, he supervised a team of LSPs providing direct support to the PSOM Office of the Dean and PSOM Leadership. In addition, Brian played a key role in overseeing identity management roll out at PSOM, managing PennKey deployment, and overseeing the email administration team.

Brian holds a Bachelor of Science degree in Computer Information Systems from Widener University. His years of focus on customer service, knowledge of the research community, and relationships with university leadership make him an ideal addition to the PMACS research team. In this new role, Brian will report directly to Meredith Fetters and join the SIO team alongside Jerry Brennian and Vince Frangiosa helping to support and enable PSOM research needs.

New Release of PSOM Faculty Salary Increase Application

The PMACS software development team is excited to announce a major new release of the PSOM Faculty Salary Increase application. The new version addresses several concerns, including relying on outdated technology and not interfacing with Workday.

Leveraging the strong partnership between the software development team and Decision Support and Analysis (DSA), the new application was rebuilt from the ground up to simplify the Salary Increase process. The new application has a user-friendly interface that makes the salary increase process easier to understand. The new application also interfaces directly with Workday, eliminating redundant data entry and reducing the potential for errors. Previously, in the old system, once the salary increase process finished and the changes were approved, the user had to manually re-enter the information into Workday. With the new application, salary increase data is transferred directly into Workday through the interface.

HPC Improves Performance With Spring Upgrades

The PMACS High-Performance Computing environment is excited to announce several recent upgrades and additions over the past several months. With the addition of new resources this spring, the HPC is now taking advantage of last fall’s InfiniBand network upgrade of handling internal data transfers at speeds up to 200 Gbps. The first new resources to connect at 200 Gbps are two GPU nodes, each with four NVIDIA H100 GPUs (80GB memory per card). To connect to the newer switches, the operating system on the new GPU servers is Rocky 9. The second resources to connect with the new InfiniBand fabric at 200 Gbps is 4.1 PB of new storage. This effectively doubled our capacity when it came on-line during April’s Quarterly Maintenance downtime.

Later this year, the existing HPC resources will be upgraded from CentOS 7 as part of a major upgrade initiative to ensure the cluster’s longevity.

Research Information Systems Harmonize New and Legacy Data in Common Systems

As new, modern electronic systems are brought online to support research in PSOM, many labs find themselves with older, legacy data that is still important, but difficult to access. Teams within the Research Information Systems area help to make this data more valuable by migrating the old data into new systems so that queries over data can be in one place, rather than running multiple and trying to combine the results.

On the LIMS team, two large data sets were recently loaded into Penn’s enterprise LIMS system, LabVantage. In the first, data for the Cancer Risk Evaluation Program (CREP) was cleaned and migrated from an old database into LabVantage, adding approximately 33,000 sample records to the system. Working together, the Gene Therapy Program and the LIMS team imported an additional 23,000 inventory items that were previously tracked in Excel spreadsheets. Adding this additional data has made it easier for LIMS users to view and track the status of their samples and inventory in a central system.

The Clinical Research Information Systems (CRIS) team has been working with the Abramson Cancer Center Clinical Research Unit Office of Regulatory Affairs (ACC CRU ORA) for the past four years on a different data migration project. This effort has focused on the migration of legacy documentation stored on the department shared server to the electronic Investigator Site File (eISF) cloud-based application, SiteVault Enterprise (SVE). Documentation from approximately 400 trials across 14 disease area teams were prioritized and imported in a multi-year migration effort. The ACC CRU ORA team cataloged all documentation and in collaboration with the CRIS team, devised a program to methodically classify all documents and apply relevant metadata to aid in search and reporting in the eISF. As of April 2024, 12 teams were successfully migrated to SVE accounting for over 350 studies and 175,000 documents. The adoption of SVE has enhanced the efficiency with external collaborators on site monitoring and forced real-time health authority inspection readiness in a 21CFR Part 11 compliant system.

A final example of a legacy data migration project is with Lancaster General Health (LGH) into the PennCRMS. The CRIS team successfully cleaned and migrated data pertaining to LGH's current research studies along with their legacy data into PennCRMS. This transition not only resolves previous challenges encountered with LGH's older research data management processes, but also consolidates over 43K patient records into a single, comprehensive platform. Consequently, researchers now have seamless access to LGH's research via the PennCRMS, which integrates research studies and patient information. This integration marks a significant milestone in our journey towards consolidating data management processes and tools with LGH. By centralizing our data within PennCRMS, we are empowering our researchers with the tools they need to drive innovation and make informed decisions.

The Best Way to Get Help? Use the Helpdesk!

Everyone from lab researchers to administrators to those of us in IT have been there: suddenly something is not working on your computer. You have tried unsuccessfully to fix it on your own and need to call for reinforcements from IT. For many, their first instinct is to reach out to the person who saved the day last time. They fire off an email…and wait.

Sometimes that can work out, but other times that person is busy helping someone else, or in a meeting, or off for the day…or week! This is the danger of a single point of contact and one of the reasons you should be reaching out to the appropriate helpdesk that is monitored by teams of people who can make sure that your issue gets addressed.

There are other reasons why opening helpdesk tickets helps everyone. Status updates and a history of the problem and resolution allow users to look for updates in one place, allow other members of the support teams to step in if times are busy, and even provide a place to search for how problems were solved in the past to help address problems more quickly. Tickets also help both the users and support teams assign priorities so that urgent matters can be tackled quickly, and low priority items can wait a little longer (say a new account you just need created in the next couple of days).

Finally, the metrics around how many new and open tickets a team has provides valuable feedback that helps managers deploy their resources and justify staffing requests.

To wrap up—Help us help you and use the helpdesk to ask for help!

Some helpdesks and which ones are appropriate for various systems:

PMACS Service Desk (PSOM, KACE)

  • PMACS Client Services
  • LIMS
  • PennCRMS
  • REDCap
  • Veeva
  • Xybion

IS Self-Service Portal (UPHS, Athena)

  • PennChart Research

Please Check Your PennBox Primary Email Address

The University is implementing an important set of changes in 2024 to the PennBox platform, which is widely used to share and collaborate on documents and data. The first of these changes takes place in May and is focused on ensuring that all individual PennBox accounts use a primary email address in the format

Users with a primary email address that is not their should change their primary address as soon as possible. If you have another email address, such as an address, you can always add this to PennBox as a secondary email address.

Individuals whose accounts are not following the standard will receive a direct communication later this spring. The last day to make changes in PennBox to your primary email address will be May 21, 2024. After that, individuals will no longer be able to make changes on their own.

For more information on how to update your email address, please visit the PMACS PennBox website.

Be Cyber Aware of Social Engineering

Social engineering utilizes deception, manipulation, and exploitation of trust to trick individuals into exposing their personal or company’s systems to malicious objectives. These attempts may include phishing emails pretending to be from trusted sources within the organization, phone calls impersonating employees, or even physical attempts to gain unauthorized access to facilities. Here are some examples that Penn Medicine has recently identified:

  • LinkedIn profiles impersonating legitimate employees.
  • Scam letters or faxes impersonating legitimate pharmacies.
  • Scam letters or faxes impersonating physician practices.
  • Phone scams.
  • Text messages impersonating employees, colleagues, or executive leadership.

Whether they are trying to extract information, money, medications, or other targets; we rely on our workforce to carefully consider unusual contacts and notify Cybersecurity when something is suspicious.

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