PMACS Penn Medicine Academic Computing Services

PMACS NewsletterFall 2022

Tuesday, December 6, 2022

Leadership Thoughts

photo of Christine Vanzandbergen

The start of a new academic year has brought a renewed energy to campus and an onslaught of new projects for the Information Services team. This fall there have been several significant projects and milestones to share, including the launch of Veeva QualityDocs in the Gene Therapy Program. We have also started migrating limited performance computing cluster users to a new storage platform that promises new functionality that will make it easier for research teams to work with even larger data sets. We now have over 3 million samples being tracked in our Lab Information Management System (LIMS). The establishment of our monthly Honest Broker workgroups and expansion of our research network for the request and downloading of data sets are examples of how we are also increasing the pace and synergy within research analytics.

Recognizing that hybrid work arrangements will continue to be a part of our work environment, we have kicked off a process to improve upon how technology can support our faculty, staff, and students whether they are working on campus or around the world. The goal established for this process is to create recommendations that will reduce friction and make collaborating easier.

Finally, the University has continued to prepare for the launch of the new Workday Learning Management System, which goes live in early spring 2023. Once Knowledgelink is replaced with Workday LMS, it will be easier for managers and employees to see performance, training, and skills data in a single system. More information will be coming in our winter newsletter, so stay tuned!

Gene Therapy Program’s Vector Core Adopts Veeva QualityDocs

PennVault QualityDocs is Penn Medicine’s web-based solution used for document management for manufacturing, clinical trials, non-clinical human subject research, and systems validation.

The Gene Therapy Program’s vector core went live in QualityDocs on October 10th, 2022, after 18 months of project discovery, ongoing requirements discussions, and application development.

The Gene Therapy Program’s vector core designs, produces and analyzes viral-based vectors used for treatment of genetic diseases. Many of the vector core’s processes are highly regulated (subject to Preclinical, Good Laboratory Practice (GLP) and Good Manufacturing Practice (GMP) regulations). For this reason, many business processes currently use paper-based, wet-signed documents as source records.

Veeva Vault QualityDocs is a one-stop platform for document authoring, revisions and approval, and contains built-in capabilities around document versioning, electronic signatures, audit trails etc. Working in regulated space, QualityDocs must be CFR 21 Part 11-compliant. Veeva provides some technical capabilities and procedural controls, while others had to be met and formally validated by GTP Vector Core.

During the project, the PennVault IS Team worked with GTP stakeholders, fleshing out configuration and processes to meet their business needs. Among the items successfully addressed are:

  • Custom Build: IS created a wide range of custom document types, fields, objects, lifecycles and workflows.

  • Document Migration: IS worked with GTP document specialists to develop a new standardized process to load existing GTP documents into QualityDocs with new custom fields and relationships.

  • Authentication: IS worked with Penn security to create, test, and roll out a new SAML configuration to authenticate users with PMACs as identity provider to address Part 11 compliance. This method of authentication will now be available for all vault domain users.

  • User Provisioning: IS developed new process to automate user account provisioning and permissions for go live.

  • Validation: IS participated in GTP’s validation efforts, supplying them with existing validation documents and testing and documenting new and existing system build via formal processes.

  • Change Control: IS worked with QualityDocs governance groups to facilitate approval of changes to system requested by GTP.

  • Build Tracking: IS developed and used new standardized formats for tracking build items in order to accurately reproduce the non-production application functionality in production.

During the project, GTP and Information Services staff developed a very close working relationship. The IS staff learned about stakeholder business needs and how to address them from a technical standpoint. GTP in turn learned more about system capabilities, features, and how to implement and deploy validated electronic systems.

Penn+Box Announces New Storage Limits, Data Archiving Process

Following up on the December 2021 announcement regarding the introduction of storage limits to Penn+Box, ISC (in consultation with numerous stakeholders) has made revisions to the storage limits previously announced. The new limits are described below and will only affect 0.2% of all PSOM faculty, staff, and students. ISC will also introduce a new de-provisioning and archiving process to ensure the removal of users who have left the University of Pennsylvania from the service.

New storage limits for PennBox accounts

Effective October 18, 2022, new storage limits in PennBox took effect.

  • Users with less than 1 TB of data now have a limit of 1 TB.

  • Users with more than 1 TB of data but less than 5 TB now have a limit of 5 TB.

  • For users who exceed the 5 TB storage limit, upon further review, higher storage limits will be offered at an additional cost starting in FY2023*. No limits have currently been implemented on these users.

Users who exceed their storage limit and would like to request a change should submit a PMACS / DART Helpdesk ticket or contact their LSP.

*Storage costs will be determined by end of calendar year.

Process for periodic deprovisioning and archiving

Effective October 25, 2022, a new rolling account de-provisioning and archiving cadence, with a three-month account and twelve-month data management interval process, will be put into place. Accounts that are no longer active at Penn will be archived quarterly and purged after 12 months unless another Penn user contacts their LSP to request the data be transferred over.

To reduce the possibility of losing data, individuals should transfer ownership of their Box content to another user before they leave Penn. Instructions can be found on the Box website.

More information can be found at the DART website.

Questions or concerns can be directed to the PMACS/DART Website’s Need Help page or your PMACS / DART SIO.

LabVantage LIMS Adds Billing Support for Core

A challenge for any core providing services to Penn Medicine researchers is being able to accurately and efficiently bill for the services they provide. Typically, this means that services performed on behalf of a core’s clients are tracked in either a separate system, in Excel, or on paper. The records for these billable activities are then transferred to a billing system. This often results in double entry of work by the lab staff who have to complete and document the work and then also document that it needed to be billed.

Over the past several years, Penn Medicine’s enterprise Laboratory Information Management System, LabVantage LIMS, has grown its scope to help meet client needs in multiple lab operations areas.  Inventory tracking and equipment management are two examples of services beyond sample tracking that the Penn Medicine LIMS Team has implemented for various clients. In response to requests from several of the cores supported by the LIMS team, billing support is the most recent addition to the portfolio of capabilities offered.

The LIMS team was able to leverage the configuration capabilities of LabVantage and add a few custom triggers to implement support for billing of core services. The benefit of adding this capability within the LIMS system is that the billable services can be tracked automatically as laboratory staff carry out their normal sample processing activities within LabVantage. For example, a core that is processing blood samples for immune profiling uses LabVantage to track the parent and child sample type, the barcode IDs for all of those samples, who processed the samples, and where they are stored.  The new billing capability simply adds a billable service record as part of this normal processing.

At a time of their choosing, the administrative team for the core can query to find all of the outstanding billable services for a particular client and gather them into billing report. While the system is designed to be generic, all of the cores currently working to implement this capability also use the iLab platform for billing, and LabVantage has been configured to generate a file that can be loaded directly into iLab to carry out the financial transactions. This design provides an excellent separation of responsibilities and allows LabVantage to focus on the laboratory process and collecting records of their completion and iLab to focus on the financial details such as budget codes and integration with the institution’s financial systems.

The first core is expected to begin using this capability in October 2022 and two others are aiming to take advantage of these new capabilities in the coming months.

Liquid Nitrogen Project

The PMACS Application Development team is piloting an application for the Cryogens Facility to streamline their liquid nitrogen and dry ice services.

Replacing an email ordering process, the new application will provide a centralized system that allows customers to enter tank information, create refill and subscription orders, and monitor historic and upcoming deliveries for liquid nitrogen and dry ice. This will remove the need for the facility to initiate these actions on the users’ behalf while providing additional insight to users. The application will also introduce greater flexibility and visibility into the delivery process for the facility administrators and delivery experts.

To simplify the billing process, the app has been integrated with the Central Account Management Services (CAMS) application to allow for the administration of the billing process directly from the application. Integrating the billing with the order and delivery functionality allows for adjustments and order modifications to be automatically tracked and reflected, instead of manually maintained, during the monthly billing cycle.

The development team looks forward to helping the Cryogens Facility realize these efficiencies and create additional benefits going forward.

PSOM Purchase Program Continues to Simplify Windows PC Purchases

During the early days of the COVID-19 pandemic, PMACS / DART introduced a small PC Purchase Program to help quickly deploy new computers upon the request of departments, centers, and institutes. Over the previous two years, this program has grown and expanded.

PMACS / DART maintains a stock of new Dell laptops and desktops. Anyone who would like to purchase a computer can do so by submitting a purchase request here: You must supply a 26-digit budget code when placing your order and the contact information for your Business Administrator.

Laptop: Dell Latitude 5430
12th Gen Intel Core i5-1235U
512 GB SSD
14" FHD (1920x1080) Non-Touch
Current Price: $1,500

Desktop: Dell OptiPlex 7000 Small Form Factor
12th Gen Intel Core i5-12500
8x DVD+/-RW
Current Price $1,100
Note: Desktops do not include monitors.

If you have any questions, please contact your LSP or submit a PMACS / DART Helpdesk ticket.

How to Catch a Phish

Recently, Cybersecurity sent out a monthly simulated phishing email that tripped up more people than usual. Since most security incidents involve a phishing email, this newsletter discusses some ways to spot a phish if one lands in your inbox.

Below are some clues that an email is likely fraudulent:

  • Check the sender’s address –

    • Do you know this person? If you’re not expecting an email from someone, consider reaching out offline to the person via a phone call to check if this is authentic.

    • Does the email address seem legitimate? Look at the “domain” (the second half of the email address after the @ symbol). Are there typos or clever misspellings?

  • Does the subject say [External]? This means the email came from someone outside of Penn Medicine, and this is a hint to treat this message with more caution.

  • Context clues that don’t make sense in the message –

    • Is this a normal request from this person, or is this out of the ordinary?

    • Is the tone of the email different than usual? (eg, are they rude? Unusually friendly? Do they insist you rush to respond?)

  • Misspellings, grammatical errors, blurry logos, or poor design in the email. These can indicate an email is not legitimate.

  • Links that don’t match where they say they are going. Remember, hover over a link to see the actual destination. And if you aren’t familiar with this website, don’t click the link!

Thanks for staying alert when opening emails – most successful data breaches start with a phishing attack. Keep Penn Medicine safe by not getting caught by a phish!

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