PMACS Penn Medicine Academic Computing Services

PMACS NewsletterWinter 2024

February 5, 2024

Introduction / Leadership Thoughts

As 2024 begins, it is a time to reflect on the successes and challenges of the previous year, as well as look ahead to the vision for 2024 and beyond. There is much to be proud of in 2023, with the continued partnership between PMACS, researchers, clinicians, faculty, and operational colleagues in delivering technology and solutions. In 2023 we embraced the name PMACS, going back to our roots as the Penn Medicine Academic Computing Services team. There was a focus on updating the team structure by bringing on a new Associate CIO of Research Information Systems, Meredith Fetters, as well as the establishment of a new Project Director for PSOM Administration, Doug Brunk, and a new Sr. Director of Research Information Systems, Ned Haubein. Jerry Brennian was brought on to the team as a new Service Information Officer as well.

These enhancements to the team structure further enable our ability to execute on the key initiatives supporting research and PSOM. From a systems perspective, the focus for the year was on growing and expanding the reach of existing systems such as increasing the Penn Medicine Biobank, implementing Immune Health billing and assay support, and standing up Gene Therapy Program manufacturing support in LIMS. In addition, 2023 saw the successful upgrade of the Velos CTMS platform and the implementation of Site Vault at Pennsylvania Hospital. 

Looking ahead to 2024, we will focus our efforts on aligning with the recently published strategic plan by working to onboard regional hospitals into central research systems like LIMS and CRMS and helping drive physical movement of research samples across the health system. In addition, the teams will work to simplify and standardize access to EHR data for researchers, further support data integration in cloud computing environments to maximize data value, and coordinate with PSOM and Health System leadership to make computing resources and data storage more easily accessible. We look forward to continued collaboration and execution with our colleagues in 2024! 

Staff Spotlight

Announcing Doug Brunk’s Role as Project Director for PSOM Administration

Douglas Brunk has taken on a new role as Project Director for PSOM Administration and started in July 2023. In this role, he liaises between Corporate IT and PSOM Administration. He works closely with PSOM Administration senior staff to identify and design solutions and with other IT teams to address the school's needs.  He also plays a technical leadership role within the Decision Support team in PSOM to help with project management and best practices. He reports to Meredith Fetters. 

Doug joined the PSOM IT team in 1991 as a developer of education software for medical school students. During his 30+ years in Penn Medicine, he has assisted with desktop support, built and managed the first web development team, managed the systems administration team, directed the software development team, and worked with the DAC on data quality and PSOM reporting initiatives. 

Doug has an MS in Information Science from Drexel University, focusing on software and database development and design. His long-standing commitment, relationships, and intimate knowledge of PSOM put him in a unique position to assist with the administrative needs of the school. 

Announcing Jerry Brennian’s Promotion to Service Information Officer

Photo of Jerry BrennianJerry Brennian has been promoted to the role of Service Information Officer within PMACS. Jerry will be reporting directly to Meredith Fetters and will bring much needed help to the SIO Team. Jerry joins Vince Frangiosa and a yet to be named third SIO.

Jerry joined PMACS in 2010 as a Local Support Provider (LSP) where he provided excellent service to PMACS users for 6 years through hard work and keeping a customer first approach. In 2017, he was promoted to Project Manager after leading several successful projects as an LSP. As Project Manager, he has led many school-wide projects including the Office 365 Migration, transition to PMACS internal network, and modernization of PMACS asset management. He was also a vital part of the team that led the transition to work off-site and the implementation of Zoom.   

Jerry has a BS in Information Science and Technology from Penn State. His steadfast commitment to customer service and intimate knowledge of PSOM will be a great asset in helping support the research mission in the future. 

PMACS Launches Two New Applications for the Abramson Cancer Center CCSG API / RBA

The PMACS Software Development team is in the process of re-writing the Research Billing Application (RBA) and wanted to provide a way for the Abramson Cancer Center (ACC) users to easily auto- populate select data (i.e. Title, PI Sponsor) needed for the application form. By leveraging an existing application called Cancer Center Support Grant (CCSG), which stores the cancer’s entire clinical trial portfolio, the team built an API that could be leveraged to load these data elements. The API saves ACC users time and reduces data entry errors.

Oncology Protocol Active List Application

The Oncology Protocol Active List (OPAL) application is designed specifically for physicians and researchers’ teams to search and see all open and enrolling cancer-relevant adult studies. The ACC adult clinical research portfolio includes research protocols from all Penn Medicine-owned adult hospitals and ambulatory centers, as well as all 12 University of Pennsylvania schools. Data is refreshed twice a day and when a study closes to enrollment, it disappears. If a study temporarily closes, it will disappear and reappear when re-opened. Anyone with an active PennKey can login to search the portfolio!

This project also included cross-collaboration with the design team, who created a beautiful visual interface for us in one week!

PennCRMS Upgrade Supports Future Growth

On Saturday, January 13th, PMACS and Velos successfully upgraded to version, positioning Penn Medicine and PSOM to adopt future functionality to better support the clinical research mission. PennCRMS currently supports over 8,800 studies with approximately 550,000 research subjects and almost 850 active users. PennCRMS is a core component of Penn’s clinical research systems.

PennCRMS, Penn Medicine’s Clinical Research Management System, provides a broad array of benefits to study teams, departments, and Penn Medicine: 

  • Study coordinators, principal investigators, faculty and research staff can track and report on subject tracking, Clinical Research Form (CRF) collection, data collection and management, reporting, calendaring, and finance.  

  • Departments can report on enrollment metrics, study progress, and financial status. 

  • PennCRMS can help facilitate rapid study activation. 

  • PennCRMS is 21 CFR Part 11 compliance, a key requirement for research projects subject to FDA oversight. 

  • PennCRMS interfaces with PennChart EHR by synchronizing patient enrollment statuses between the two systems, creating one consistent source of enrollment data. This means that study, patient, and demographic data remain current and accurate in both systems.  

The upgrade project required close communication, hard work, dedication, and teamwork from the PMACS Clinical Research Information Systems (CRIS), LIMS and infrastructure teams, the Office of Clinical Research and the vendor, WCG Velos. To continue to support 21 CFR Part 11 compliance, the team had to work together to complete several steps, including documenting every step of the upgrade process, then reviewing and approving all documentation with business, technical and quality assurance leaders.  

Thanks to the hard work of the project team, users were able to log into a fresh, new application with streamlined workflows by Monday morning! 

If are interested in learning more, please contact to learn more.

PMACS Teams Support Collaborations with External Sites Using LabVantage LIMS

When launched at Penn Medicine, LabVantage LIMS was initially focused on supporting individual laboratories at Penn. The system focused first on biobanking, eventually expanding to include central labs, the movement of samples among collaborating labs, and finally other areas such as billing support and managing high value inventory and equipment.

The LIMS team also supports research partners is cooperation with external laboratories. Two recent examples highlight how LIMS approaches external collaboration.

Data Transfer

The first example involves a dermatology lab where legacy data and samples were housed at the National Institutes of Health but needed to be transferred to Penn Medicine to preserve them for future research. The LIMS team brought deep experience in legacy data migrations to the project. Working with the Penn laboratory and the NIH, the team developed a plan to identify and extract the relevant data from the source system and transform and load the data into LabVantage. This process involved extensive validation and cleaning of the data to ensure its accuracy. A standard import tool developed at Penn was leveraged to load data for 25K samples. All existing barcodes were imported to LabVantage, which was critical to the project because this eliminated the need for the study team to re-label all the samples. This project was very successful in bringing the samples and data to Penn in an orderly way to enable future research.

External Collection Sites

In the second example, Penn is the sample coordinating center for an active OB-GYN study that will be receiving samples from both Penn and external collaborators. Because Penn will be receiving pre-processed, frozen samples, its important that external sites pre-label samples with LabVantage barcodes. However, experience has demonstrated that ensuring all sites have and use the correct labels for all participants is challenging.

Working with the lab at Penn, the LIMS team developed a process that would enable the lab to send sample labels un-associated with specific participants to the sites in bulk. The participant ID is later written on the sample and included in an electronic manifest when returning the sample to Penn. This process allows the lab to have multiple checks to ensure the sample is mapped to the correct participant. The electronic manifest includes sample locations within each box and is imported to LabVantage. The result is that the Penn lab stores boxes of samples upon receipt instead of filing individual samples.

This approach is already being adopted by other laboratories, as the approach the strikes a balance between accurate electronic annotation and practical considerations of working across multiple teams and institutions.

If your lab has interest in migrating to LabVantage, please contact to learn more.

Phishing with QR Codes: A New Cybersecurity Threat

Cybercriminals are using email-based quishing attacks to target users. Quishing, also known as QR code phishing, is an emerging cybersecurity threat that exploits the convenience and trust associated with QR codes. Attackers create deceptive QR codes to lead victims to phishing websites or initiate harmful actions on their devices. You can protect yourself by verifying the source of QR codes, using secure QR code scanner apps, inspecting URLs, enabling two-factor authentication, education, and reporting suspected attacks.

Stay vigilant and cautious when scanning QR codes to mitigate the risks posed by this evolving form of cyberattack. For more information, visit the Cybersecurity website under Training & Awareness “How to prevent Quishing- QR Code Phishing”.

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