Penn Medicine Academic Computing Services


IS Leadership Insights from Brian Wells

Leadership Thoughts

Innovation is often achieved by applying existing technology to a new problem. In late 2012 when Penn Medicine IS identified the need to unlock the millions of unstructured textual documents and data items within our electronic medical records and diagnostic systems, we began searching for an existing tool - one that solved a similar problem in a different industry. We knew that our researchers and clinicians needed to be able to simultaneously, effortlessly and intuitively search through large amounts of unstructured data but also have the power to filter results using discrete data from our clinical data warehouse, Penn Data Store. We learned of a tool used by many popular shopping web sites (Lowes for example) that made it very easy and blazingly fast to search through large product descriptions and discrete attributes to find the ideal product. By thinking of patient data as product data we realized we had a perfect fit. From this eureka moment, combined with the very creative contributions of members of the Penn Medicine Data Access Center (DAC), arose what we now call PennSeek.

On April 28th, a submission describing PennSeek to the Information Week Elite 100 Innovation competition (an annual list of the best U.S.-based users of business technology) resulted in Penn Medicine ranking in the top ten overall and first among healthcare organizations. We have achieved well deserved recognition for Penn Medicine and at the same time are leveraging the investment Penn Medicine has made in electronic medical records for the benefit of our patients and research subjects. It is an honor to be a part of this accomplishment.

HPC Stats — March 2015

  • CPU Hours 1,536,139
  • Disk (TB) 1188
  • Archive (TB) 116.4
  • Total Number of Users 218

Technology Initiatives


Network Integration

Current State

Within the university computing environment, the university’s Information Systems and Computing (ISC) department manages the network (PennNet). Unlike the UPHS network (UPHSNet), PennNet is an open network with connected computers and printers having public internet addresses. Also, there is no main firewall on PennNet that protects all connected devices from external attack; firewalls are instead deployed at the server level.

Most PSOM employees and some UPHS employees rely on the PennNet network for access to data and systems. With increasing integration of Penn Medicine’s clinical and research missions, there is an acute need for enhancement of the PSOM network to ensure more secure connectivity with UPHSNet. Therefore, PMACS will be implementing, with ISC’s assistance, a new sub-network inside PennNet for all PSOM or UPHS devices connected to PennNet. This sub-network, dubbed “PennMedNet”, will increase the level of protection for PSOM and UPHS user devices as well as data and applications.

Future State

As shown in the following figure, we will consolidate the various PSOM network segments behind an enterprise-class firewall and VPN (Virtual Private Network) appliance. These tools will enable over 50 existing firewalls to be retired. The consolidation of the network segments will be achieved by use of several additional firewalls in the PennNet routing core.

Network Integration

The benefit of these changes will be the creation of a private virtual network (PennMedNet) that is more secure and accessible only by trusted Penn Medicine (UPHS and PSOM) users and resources.


Creation of PennMedNet would be completed in phases as defined below:

Phase I
  • Purchase and implementation of enterprise-class firewall appliances.
Phase II
  • Installation of PennMedNet firewalls in ISC core routing
  • Creation of routing rules for true internet traffic (e.g., Google search, accessing NJEM) and Penn Medicine traffic, PSOM and UPHS
Phase III
  • Creation of secure network link to UPHSNet
  • Consolidation and retirement of existing point-to-point network interfaces

The project will be completed by December 2016.

Account Consolidation Update

As quickly as Penn Medicine grows and expands, its core values have not changed. One of these values is collaboration, which becomes more prevalent each day in the Perelman School and UPHS.

As collaboration has expanded, so too has the need for information to be shared among groups. The increased need for shared information currently makes the user’s experience more complex, requiring additional sets of user credentials to access computers, servers, data stores, and other electronic resources. We are excited to be moving forward on an organization-wide consolidation project that will greatly reduce the number of user accounts required to access any of these resources.

Much of the work required for the consolidation project to occur is being done with no impact on the daily workflow of the users. As we move forward with the migration of users, the goal of minimal impact will be accomplished by scheduling impactful process during night and weekend hours. This will allow us to make the migration as seamless and transparent as possible. In fact, The Center for Clinical Epidemiology and Biostatistics (CCEB) has already been migrated to the PMACS domain and users noticed minimal impact.

User benefits include:

  • Migration – current desktop is migrated with no impact on your current profile settings
  • Single User Account Sign-on Capability – single username and password for PMACS resources
  • Improved Service/Reduced Complexity – single set of user and computer policies
  • Self-Service Capability for your Domain Account – web based password reset portal
  • Expanded Collaborative Capability – ability to share resources across Penn Medicine
  • Increased Security for your Computer and Data


Brief History of Virtual Curriculum 2000

The Penn School of Medicine (PSOM) launched Virtual Curriculum 2000 (VC2000) in 1998 as a learning management system (LMS). PSOM was the first medical school in the country to have on-demand content delivered to its students. Over the ensuing decade there a shift has occurred with the advent of mobile and handheld devices – presenting a growing need for a mobile compatible LMS. In the interest of moving toward achieving this need, PSOM decided to acquire a modern LMS to replace VC2000.

Transition from VC2000 to Canvas – A Brief timeline

  • Spring 2012 – The process for LMS requirements began.
  • Fall 2012 – Request for Proposals (RFP) were sent to selected vendors.
  • Spring 2013 – Vendors were requested to visit on-site and demonstrate their LMS for our users.
  • Fall 2013 – After all the submissions were reviewed and found to be incapable of fulfilling the medical school’s needs, the decision was made to not use any of these vendors.
  • Winter 2013 – The Canvas LMS was reviewed and vendor selection was made.
  • Spring 2014 – The integration with Canvas and our Student Information System (SIS) began.
  • Fall 2014 – A Canvas pilot for two courses was run in December 2014.
  • Spring 2015 – The full rollout to Canvas for School Teaching Modules 2, 3 and 6 began.
  • Summer 2015 – The remaining modules will be migrated to Canvas.


The main challenge was to seamlessly integrate our student information system (OASIS) and school events with Canvas. PSOM is different from other schools due to the nature of its course structure. A large number of individual courses are tied together in “modules” that every student takes together at the same time. Unfortunately, traditional LMSs like Canvas require a different approach for course management based on the semester concept. The challenge was to enable OASIS to be able to feed course enrollment and event data transparently into Canvas to enable a single point of student entry.

It had been hoped that when each individual student logged on to Canvas that their personal touch down page would be a weekly calendar that listed all their lectures, small group teaching, and other school events. At this time this has not be been accomplished, but discussion with the Canvas owner and programmers are underway.

In addition, a number of applications used by PSOM such as Mediasite (A lecture capturing technology) and iSEEK (A targeted search engine for medical databases, lecture documents and videos across the medical curriculum) have to be integrated into the system.


In general the students have been pleased with Canvas and there have not been any major issues. Course lectures and materials can be downloaded. The complete transition to Canvas will be a yearlong process, and as noted above, we are hoping to move the remaining courses into Canvas during summer 2015. It is also hoped that a fully integrated student calendar will be able to be developed.



Over the past few years, the PMACS department has worked to centralize biosample management activities in PSOM. Many labs and studies have no efficient system to track the hundreds of thousands of tissue, blood, and other sample types collected and used during research studies. Unlike most clinical lab systems, a research lab management system generally has the capability to track samples and test results, but also to track sample locations over a long period of time. This biobanking feature allows for samples to be collected, analyzed, stored, and used at a later date based on current and future study needs. Over the past three months, a number of labs/studies have gone live on PennLIMS, and several new labs/studies are scheduled to go live over the next few months. Recent studies that have gone live are:

  • Gastroenterology FARMM Study/Dr. Gary Wu: This study protocol requires the collection of many hundreds of samples from each research participant over the course of several weeks. PennLIMS handles the barcoding, tracking, and long-term storage of these samples.
  • Schellenberg Lab: Dr. Schellenberg in the department of Pathology and Laboratory Medicine has a number of existing samples managed using a legacy system. Dr. Schellenberg’s lab was setup on PennLIMS, and they are using the system to manage their current and future study samples.
  • Busch Lab/Radiation Oncology: Dr. Busch’s lab was setup on PennLIMS, and is using the system for new and existing samples.
  • Radiation Oncology/Dr. Hahn: A Phase II go-live to an existing PennLIMS lab, the study protocol requires samples be sent to the NCI. PennLIMS will manage these offsite samples and storage locations, providing for a comprehensive sample inventory for the lab.

Lab studies in progress are:

  • Rheumatology Lab/Dr. Merkel: Dr. Merkel’s lab has a current inventory of approximately 250,000 samples, and the labs collects and pulls hundreds of samples each month. Currently using a legacy system built and managed elsewhere, the lab sought an on-premise, sustainable solution. Work is underway to migrate all existing samples, and sample data, to PennLIMS.
  • Gastroenterology/March of Dimes Study/Dr. Gary Wu: Dr. Wu’s March of Dimes study has been recently approved, and work is underway to create that study in PennLIMS, in preparation for sample collection.
  • Investigational Drug Service/Dr. Rockwell: The Investigational Drug Service provides services to the University at large, including PSOM and the Veterinary school. A project is underway to migrate their current sample tracking and assay management system from a legacy database to PennLIMS. Unlike existing labs and studies, the IDS operation is managing sample assays, and this capability will be integrated into PennLIMS for the tracking of assay results. This will be the first instance of assay management within PennLIMS.

User Tip

Top Ten Imposter Scams

Scammers are all over the internet just waiting to prey on unsuspecting individuals who are willing to give up their personal information. The FTC recently released the following listing of the top ten imposter scams for 2014:

  1. IRS Imposters. The real IRS won’t initiate contact by e-mail or phone, they will start with a postal letter.
  2. Surprise? A prize patrol contacts you about winning a large sum of money; only thing is you need to send them some money to collect your prize. Don’t believe it.
  3. PCs R Us. Someone contacts you to inform you that your computer has a serious technical problem which they can solve for you. Not true.
  4. Mal-Where? Someone calls pretending to be from Microsoft or other Technical Support and says there is dangerous software on your machine. Just click on the pop-up that may be on your screen. Don’t.
  5. Fake Fed. Similar to the old Nigerian e-mail scam, only now a fake federal agent is confirming that Nigerian royalty really does want your help to move a large sum of money out of their country.
  6. Kidnapped Computer. You click on a link and a pop-up appears saying you have been locked out of your files. Don’t pay the ransom to unlock your files; more often than not even if you pay, the files won’t get unlocked. Tip, remember to back up important files often.
  7. Government Grants. Someone posing as a federal official tells you that you have won a government grant, really? All you need to do is pay associated taxes and fees and you will be sent the money.
  8. Medicare Disqualification. A bogus government representative claims to work for Medicare or for the Affordable Health Care Act and you will lose benefits unless you pay a fee or provide updated personal information.
  9. Deportation. A variation on the bogus government representative is a caller from Homeland Security who threatens an immigrant with deportation notices, but will help to ‘certify’ them for a fee and/or by providing updated personal information.
  10. Caller ID. A scam that spoofs caller ID in order to get you to pick up the call. In some cases this incurs usage charges.

Avoid Being a Victim

  • Be suspicious of unsolicited phone calls, visits, or email messages asking about internal information. If an unknown individual claims to be from a legitimate organization, try to verify his or her identity directly with the company.
  • Do not provide personal information or information about your organization, including its structure or networks, unless you are certain of a person's authority to have the information.
  • Do not reveal personal or financial information in email, and do not respond to email solicitations for this information. This includes following links sent in email.
  • Don't send sensitive information over the Internet before checking a website's security.
  • Pay attention to the URL of a website. Malicious websites may look identical to a legitimate site, but the URL may use a variation in spelling or a different domain (e.g., .com vs. .net).
  • If you are unsure whether an email request is legitimate, try to verify it by contacting the company directly. Do not use contact information provided on a website connected to the request; instead, check previous statements for contact information.
  • Install and maintain anti-virus software, firewalls, and email filters to reduce some of this traffic.
  • Take advantage of any anti-phishing features offered by your email client and web browser.

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