Penn Medicine Academic Computing Services


IS Leadership Insights from Brian Wells

Leadership Thoughts

Penn Medicine is poised to make a significant investment in the informatics and administrative information systems used to support the clinical research mission. Our Senior IS governance committee has recognized the opportunity to greatly enhance our IT support of clinical trial management, including improvements to integrate clinical trial billing with the UPHS electronic medical record (EMR), clinical trial recruitment activities and document management over the clinical trial life cycle. This degree of investment will be spread over several years. Together with other significant process improvements being undertaken by the Office of Clinical Research and others, this investment will result in:

  • Decreasing the time from trial conception to first patient enrolled
  • Simplifying the management and review of trial documents
  • Increasing fiscal compliance and optimizing revenue capture related to clinical research billing
  • Increasing patient's access to trials currently recruiting at Penn Medicine.

The work is beginning now in partnership with the Office of Clinical Research. We have started with the hiring of additional Epic and clinical trial management system (CTMS) IS staff as well as the establishment of project teams, oversight committees and advisory boards. Clinical research faculty and staff should expect to see changes this fiscal year in the areas of trial recruiting and gradual expansion toward enterprise use of a common CTMS. Integration with the EMR will start with sharing of patient demographic data and enrollment status in 2015 followed by billing integration post PennChart Phase II (Inpatient Epic) in 2017. An enterprise document management system (DMS) project will likely start in fiscal 2016.

This exciting group of enhancements to existing systems and brand new technologies will further cement Penn Medicine's leadership in clinical research and provide the transparency, process improvement and data analytics required to achieve our missions.

PennHPC Archive Fast Facts

  • Location: Tierpoint datacenter @ the Navy Yard, a Tier-3 facility
  • Total Storage Capacity: 3.6PB
  • Effective Storage Capacity: 1.6PB
  • Number of LTO-5 Tapes: 1,910
  • Number of LTO-6 Tapes: 280
  • Number of LTO-6 Drives: 12
  • Drive Manufacturer: IBM
  • Tape Library Total Slot Capacity: 3,570 (approximately 60% populated)
  • Tape Library Manufacturer/model: SpectraLogic/T950
  • Tape Library Configuration: One drive frame (12 drives, 12 free bays), two media frames (tapes only)
  • Archive Software: SGI/FileTek StorHouse

Technology Initiatives


New prioritization process for web design requests

The Web Design Team developed a method to prioritize web design services, which was recently reviewed and approved by the Administrative Computing Advisory Board (ACAB). We are changing our approach to enable web sites to be created and maintained more efficiently.

Submitted projects are now divided into three priority levels with associated levels of effort. Priority 1 projects include school-wide projects like the top level web pages, departmental web sites, type 3 centers, and externally facing administrative sites (e.g. Admissions or BGS). Priority 2 projects include type 2 and 1 centers and administrative web sites. Priority 3 projects include sites for faculty laboratories and student groups. Priority 1 and 2 projects will be allocated an amount of time by the team. Priority 3 projects will be eligible to select from a set of website designs provided in a self-service manner (see the following article for details).

For further information see

Self-serve web sites

The PMACS Web Design Team will soon be offering a self-serve website tool for users to independently design simple, uncomplicated websites that do not require custom professional design. Instead of working with the Web Team to customize design options and populate their site with content, those who opt for this service will be provided with standardized options and will be set up to enter the content, themselves, in return for a speedier launch.

The self-serve website service provides a choice of three mobile-friendly design templates with three color/font themes each (9 design options total), taking advantage of PMACS's new content management system, MODX. It will offer several site- and page-wide level options such as news feeds, events feeds, announcements or other featured content, page banners/slideshows, a site-wide search, and the ability to post secure pages or documents that are automatically PennKey-restricted.

Once the site owner selects a design and receives training in MODX, (s)he can populate the site on a non-public development server. When finished, the PMACS Web Team can then easily push the site live, and the site owner can continue to use MODX to maintain the live site in future.

The self-serve option caters to those who do not need assistance analyzing or organizing content and who wish to launch a simple site quickly with minimal assistance. This will be the only option available to Priority 3 projects (faculty lab and student group websites) that are looking for a PMACS-supported solution.

The Team is currently working with pilot groups to refine the self-serve service and is planning to make this option fully available in the coming weeks. For further information see



The Q-Path project will facilitate use of integrated Point-of-Care-Ultrasound (POCUS) in the Perleman School of Medicine training program. The project, led by Dr. Harvey Nisenbaum, Dr Anthony Dean, and Anna Delaney with the full endorsement of Dr. Gail Morrison, will devolop a comprehensive program to incorporate ultrasound training into Penn Medicine, the Perelman School of Medicine and the Penn Medicine health system. PMACS is working with the project team to provide the supporting server and data storage infrastructure.

Medical educators have recognized that ultrasound can be a powerful adjunct in the teaching of anatomic, physiologic and pathologic concepts. A secondary benefit is the ability of ultrasound to augment the education itself. A third and important benefit will be a better relationship with the patient during scanning. The student will have the opportunity to explain in better detail what might be wrong and describe the images to the patient.

The goal of the project is that Penn medical students, by the time of graduation, will have an understanding and competency to perform ultrasound that will be enhanced by each residency pursued.


New Opportunities for Big Data at Penn

Penn Medicine's PMACS department partnered with Dr. David Srolovitz, the Joseph Bordogna Professor of Engineering and Applied Science & Founding Director of the Penn Institute of Computational Science, to optimize the campus network in support of big data research and high-performance computing. The partnership included leading campus researchers in engineering, physics, biology, pathology, genomics, bioinformatics, and computer science.

Made possible by a grant from the National Science Foundation, this project established a 100 Gbps-capable Science DMZ that is distinct from the general purpose campus network and is engineered for research applications. Additionally, it extends 10 Gbps connectivity to select research projects and increases Penn's connection to Internet2, the national research network, from 1 Gbps to 100 Gbps, while also extending that connection to the Science DMZ. The project also lays the foundation for further enhancements to research networking infrastructure by extending IPv6 capabilities; upgrading network performance monitoring tools such as perfSONAR; and enhancing Penn's ability to support experimental networks and network architectures, including OpenFlow and Software Defined Networking.

Proposed network including science DMZ

For further information contact Greg Palmer at

HPC Archive System Service

The Penn High Performance Computing (HPC) service is a set of capabilities managed by the PMACS ERA (Enterprise Research Applications) team that provides high-speed storage, compute, and archive resources for PSOM and other University staff and researchers. Past newsletter articles have detailed the compute and storage resources the HPC system provides; this article provides additional details regarding the archive service.

The Penn HPC Archiving Service is a tape-based archive that is completely self-service for both storage and retrieval. It works just as any other directory/share to which data is written. Archive users are provided a mapping similar to any other server-based storage, and data is copied or moved to this directory using common commands such as copy/paste. Users can copy data from existing Penn HPC directories or from other network and host locations. The process of moving files to the archive is very similar to what many labs and users do when backing up their data to DVD drives, external hard drives, or USB keys. Data retrieval is equally as easy, requires no intervention from PMACS, but does take somewhat longer than retrieving data from a hard drive or USB key (since the data is read directly from the tape system).

The archive system is available to University staff and faculty, and could be configured for use by UPHS users as well, should the need arise. The system is fee-for-service based, and charged at a rate of $0.015/GB/month. At this rate, storage of a terabyte of data costs $15/month, or $180/year. Usage is based around average daily usage, so users are only charged on their daily usage, essentially pro-rating the usage cost by the calendar day. There are no charges assessed for data transfer in or out of the system, or for the actual account creation itself, only for the actual volume of storage the user consumes.

Accounts can be setup by sending an e-mail to

Update – Upgrade of Velos Clinical Trail Management System (CTMS)

The Velos CTMS, currently used by the Abramson Cancer Center (ACC), is being upgraded to the latest release of the product. Velos is used by ACC to register and track all cancer-related protocols and clinical trials. The support team is currently on track to complete the upgrade in February.

Afterwards, planning will begin for a phased integration with PennChart (Epic), Penn Medicine's Electronic Medical Record (EMR). This integration will:

  • Reduce the need to duplicate of patient demographic, visit and billing data between the systems
  • Improve physician workflow, patient safety, and billing compliance for clinical trials.

It will also be an important foundation for future improvements to the clinical trial process in ACC.

Ebola Surveillance System using REDCap

The Hospital of the University of Pennsylvania (HUP) is now a designated treatment center for the treatment of first responder health care workers suspected of and/or infected with Ebola Virus Disease (EVD). Preparations and protocols are in place to help manage and mitigate the risks associated with the infectious disease and managing this infectious disease. HUP physicians and staff are performing the vital care roles for these patients and it is essential to also have protocols in place to manage these HUP teams.

HUP, the Perelman School's Clinical Research Computing Unit (for technical programming), and the Penn Medicine Academic Computing Services (for technical systems support) have developed a self-reporting and notification application using the REDCap data capture and surveillance toolkit. This new application, the Ebola Surveillance System (ESS), will be used to ensure HUP's compliance with monitoring all involved HUP team members who have direct contact with patients with or suspected of being infected with EVD. This application will help ensure that appropriate protocols are followed to manage, report, and track if a HUP team member becomes ill during or post care of a patient with EVD.

The application is one of many protocols in place to ensure the safety of the patients, the HUP team members, and the general public. The application also provides local, state, and federal reporting as required based on federal guidelines.

User Tip

Information Security Liaison for PMACS

As part of Penn Medicine's Information Services Department, PMACS works with the department's Information Security team to protect electronic data. The Information Security team's liaison for the Perelman School is David Wargo. If you have specific information security questions or concerns, you can contact Dave at

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