PMACS Penn Medicine Academic Computing Services

PMACS NewsletterSpring 2021

Wednesday, May 26, 2021

Kash's Corner

Kash Patel

At about this time a year ago, we were asked to work remotely on a full-time basis as part of local, state, and national efforts to contain and manage the Covid-19 outbreak.  For the most part, working in the Information Services technology space affords a degree of flexibility regarding remote work.  I do want to note that we have maintained a persistent on-campus presence during this time in order to provide support for those individuals and teams that had to come into campus to work every day.  Our work has continued over the past year and overall, we’ve been able to continue delivering service and support to our research community.  Our team has been flexible and resourceful during this time in helping to preserve the mission and be supportive of the focused intense efforts surrounding Covid-19 research.  We remain at your service and, like all of you, continue to follow on-campus protocols like using PennOpen Pass, wearing masks, maintaining physical distance, and avoiding large crowds.

Application/Web Development

Congratulations to the PennOpen Pass team!

The PennOpen Pass team was recently recognized, receiving the University’s Models of Excellence award, in the category of Sustaining Penn Through COVID-19.  This category recognizes those individuals and teams that contributed directly to creating extraordinary outcomes for the Penn community in response to the COVID-19 pandemic. The PennOpen Pass Team, a cross functional group of employees from across the Perelman School of Medicine, the Health System, and the University, developed digital tools and operational processes to enable the safe return to campus for the Penn community. This team worked together to conceive, design, build, and operationalize the PennOpen Pass program and associated software products to perform daily COVID-19 symptom and exposure checking for the Penn community. Read more on the Penn Open Pass innovation that came from a sense of urgency to protect against COVID-19.

Enterprise Research Applications

LabVantage LIMS Marks a Milestone and Expands into New Areas

Graph of number of samples in LabVantage between July 2014 to May 2021Penn Medicine catalogued its first sample in LabVantage on July 10, 2014.  5 years later on September 19, 2019 the 1 millionth sample was added to the system, and just over 18 months later on April 5, 2021 the 2 million mark was crossed.
The second million samples were added in just 30% of the time it took to add the first million.

This milestone was achieved with the cooperation of many different groups of people.  On behalf of the entire LIMS team, we are grateful to the growing number of users (200+ users making 5K+ connections per month) who have embraced the system and driven this growth.  I am also humbled to be part of a fantastic team that juggles multiple projects, operates with a strong customer service focus, and takes pride and ownership in their work as they serve our clients.  We are fortunate to have strong DART infrastructure and systems administration teams supporting us and a strong, collaborative relationship with our vendor, LabVantage Solutions.

In addition to growth in the number of samples, users, studies, and groups supported, we have expanded LabVantage into new areas beyond biobanking.  Some of the key areas are:

  • Tracking clinical research collection kits: The LIMS team has worked with the Abramson Cancer Center Clinical Research Unit (ACC CRU) to implement clinical trial vendor kit management. This activity includes kit inventory and expiration tracking, kit preparation and delivery information, and dashboards and automated emails to communicate this information.  We are about half way through implementing the entire unit and have integrated LabVantage into their training programs; including Knowledge Link training videos produced by our team.
  • Critical Inventory Management: The LIMS team has developed and deployed an inventory management system for the Cellular Vaccine Production Facility (CVPF) group that helps them track what materials are in their stockroom, what materials are nearing expiration, and what items need to be re-ordered soon by tracking their orders and barcoded materials.  In addition, materials are bundled into kits which can be tracked, validated, and linked to research studies to maintain a high degree of traceability. The successful go-live for this project was November 2019, containing a combination of configured and custom features.
  • Equipment tracking: The LIMS team has implemented out of the box tools from LabVantage to support CVPF in tracking their equipment inventory including scheduled maintenance, maintenance and service history, equipment in/out of service status, and equipment location. This is accomplished using dashboards, email reminders, and work orders for service. The Investigational Drug Service is also working to on-board with this feature in addition to their existing stability and batch tracking capabilities in LabVantage.
  • Clinical Systems Integration: The LIMS team is excited to be partnering with several other groups to enable a seamless integration with clinical systems for research sample collection on studies where that is appropriate.  In particular, we are collaborating with the Penn Medicine BioBank (PMBB), the Data Analytics Center (DAC), and the Clinical Research Information Systems (CRIS, DART) teams to enable consent and blood draw orders to be captured in EPIC, processed through Cerner, scanned into LabVantage, and linked back to the clinical records so that consented individual’s information can be linked to their samples, further enabling the ground breaking research conducted at Penn Medicine.

In conjunction with this new work, the LIMS team has continued to support our existing clients by adding new studies and responding to 90 service requests per month. We look forward to continued growth in our user base and consolidation of research laboratory information support into one system, enabling collaboration through data sharing and inter-laboratory sample tracking.

Please reach out if you are interested in learning more and we’ll meet to discuss where we can help and determine a schedule for starting that process.


Penn Genomic and Phenotypic Data Platform (G&P)

A new generation research data platform was rolled out by the Data Analytics Center (DAC) in late January. The primary role of Penn G&P is to facilitate access to clinical and genomic data for the Penn Medicine research community by enabling both self-service access and streamlined execution of custom data requests by DAC and Penn Medicine Biobank (PMBB). Its main component is a clinical database implemented in the form of Observational Medical Outcomes Partnership common data model (OMOP CDM) alongside its web-based application called Atlas. This well-established data model is used for multi-center observational studies by the worldwide research community embodied in the open science healthcare-pharma-government collaborative called Observational Health Data Sciences & Informatics (OHDSI). By becoming a member of OHDSI, Penn Medicine has the opportunity to participate in highly visible research studies and compete for funding that requires utilization of a common data model.

Consulting Services/Service Information Officers

PSOM Ready Mission Continuity and Pandemic Response Team Update

The Mission Continuity teams were established for each of the 12 Schools, Health System, and the University. The use of the teams was expanded to encompass pandemic response as an extension of existing responsibilities. The inception of the pandemic required dedicated and focused responses from Perelman School of Medicine Mission Continuity team.

Multiple steps were taken to comply with Philadelphia guidance regarding COVID-19 and Universities in support of the research and education missions.

  • Depopulating our facilities
  • Sourcing PPE
  • Ensuring the proper safety measures
  • Assuring the ongoing operations of critical research and education 
  • Enabling our labs to repopulate safely
  • Creating guidance for all phases of school response to the pandemic
  • Established compliance tours for laboratory and office space
  • Respond to P-COMPLY reports and notifications of masking or distancing violations

Our mitigation efforts are working, at present we have zero reported workplace transmissions in Perelman School of Medicine.


The Isaac website has a new look!

The Isaac website has a new look!

The Isaac team is excited to share our new website (you will need to connect to the UPHS VPN to access). We have been working hard these past few months to make our site easier to navigate, provide access to a breadth of helpful resources, and improve usability.

Here’s what’s new:

  • Quick access to Self-Service Catalog (you will use your UPHS network login)
  • Link on how to access UPHS resources remotely
  • Isaac FAQs and Resources including working from home resources, PennChart Learning Library, and PennforPeople
  • Isaac Newsletter Archive with links to the web version of the newsletter and its contents
  • What’s Hot section to showcase the latest news and announcements
  • Event calendar that will share Isaac newsletter dates, Virtual Office Hour information, and major IS go-live events. Events that have additional information are “linkable” such as the Virtual Office Hours and related website links
  • Links of Interest
    We will be continually updating our content with helpful information! If you would like to request IS assistance, Ask Isaac!


Information Assurance

The Human Firewall: Physical Security

Many facets of our lives, whether at home or on the job, are captured and stored on computers. Administrative, technical, and physical controls are necessary to secure information assets, regardless of the location of our work. If physical security controls fail, the probability of having information compromised or stolen increases. This information can include patient files, grants, research data, financial records, or your own personal data. As a member of Penn Medicine, it is important to safeguard the physical security of information and where it is located.

Here are some tips to keep our information assets safe.

  • Prevent Tailgating: In the physical security world, tailgating is when an unauthorized person follows someone into a restricted area. Be aware of anyone attempting to slip in behind you when entering an area with restricted access.
  • Properly Secure Documents: Leaving sensitive documents unsecured on your desk puts the information at risk for unauthorized access or theft. The Penn Medicine Privacy Office has published several recommendations for securing paper documents.
  • Treat your laptop like cash: If you had a wad of money sitting out in a public place, would you turn your back on it – even for just a minute? Would you leave it visible in the back seat of your car? Of course not. Keep a careful eye on your laptop, securing it just as you would a pile of cash.


The Human Firewall: Securing your Computer Access

It’s important to recognize that very few office or home environments can be completely secured. Vendors, cleaning crews, landlords, service providers, and other “outsiders” may have access to your work area in some capacity. In addition, your job may require you to handle sensitive data and files that other coworkers should not be accessing. Here are two habits that you can implement that will make a huge difference both in and out of the office.

Tip 1: Lock Before You Walk

Securing your workstation or laptop is one of the simplest and most effective ways to ramp up your cybersecurity posture. On a Windows computer you can simply press the Window key + L (or Ctl + Alt + Del and select “Lock”) and on a Mac (Control + Shift + Eject) or (Control + Shift + Power).

Tip 2: Do Not Write Down Your Passwords

Password management is a huge challenge and writing down your credentials on a sticky note or sheet of paper that you keep handy in your workspace is not a safe choice. Consider creating a password that is a passphrase that is specific and unique to you. A passphrase is a kind of password that uses a series of words. Passphrases are easier to remember than a random grouping of symbols and letters combined together. A passphrase can be your favorite childhood memory or vacation experience; for example, “Surfing in Hawa11.”

Click here to watch Penn Medicine Information Security Assurance Advisor Davis Trinh describe how to identify and report a phishing email.


Cyber Espionage to Steal Data and Intellectual Property

Over the past few months, there has been a notable increase in malicious cyberactivity targeting researchers in various capacities. Recently, most cyber-attacks are directed at COVID-19 vaccine research.  Penn Medicine recognizes that a viable vaccine, along with associated research and clinical trials, is valuable intellectual property.  With countries struggling to secure an effective vaccine, nation-state adversaries have been persistent in targeting the US biotechnology and healthcare industry to enhance their own vaccine development and distribution programs. The goal of these attackers is unauthorized access to information, such as data related research proposal, drug development, manuscripts, virus testing, clinical trials, and drug manufacturing.

The two most probable attacks are either phishing or web attacks. Penn Medicine’s Information Security Team constantly monitors these activities, but we need your help to keep Penn Medicine safe from these malicious actors. We encourage every member to report potential incidents and suspected phishing emails to the Information Security Team by either:

  • Reporting the phish using the “Report Phish” Button within Outlook
  • Forwarding the suspicious email to
  • Contacting and reporting the incident to the Service Desk


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