BMIC Informatics Resources

BMIC functions as a virtual ITMAT Center, facilitating “best practices” and access to research IS and IT resources across Penn Medicine and CHOP and has, as its primary focus, the end user amongst the 800 plus members of the institute.

In parallel alignment with the Biomedical Data Coordination Core (BDCC), formed specifically to support investigators within the Abramson Cancer Center (ACC), BMIC serves primarily non-cancer investigators, although many AAC investigators play key roles in ITMAT. BMIC provides leadership and expertise identifying and assembling appropriate informatics and data coordination services for end-user investigator teams. By making carefully selected referrals to qualified technical staff in specialized units, such as the PCBI, CBMi or the software developers/database administrators within the Clinical Research Computing Unit (CRCU), BMIC guides investigators towards qualified database services, including database design, development, and management, which meet technical and regulatory compliance requirements. The value of these consolidated services will be in assisting investigators with the tools to collect and organize clinical and translational research data by creating optimal data coordination resources, beginning with the earliest stage of study design.

Thus, BMIC provides services for ITMAT investigators along the full research continuum, including:

• data resource needs assessment;
• evaluation, selection and deployment of commercial software tools (eg, REDCap, Velos, Oracle Clinical);
• development of specialized software systems;
• support for data collection, management, and integration;
• guidance on computing hardware support and
• education and training.

BMIC will also promote integrated trans-disciplinary approaches to meeting data acquisition and storage needs of ITMAT investigators and their research teams.

Penn Center for Bioinformatics (PCBI):

The Penn Center for Bioinformatics (PCBI) is the central hub for bioinformatics and computational biology research at the University of Pennsylvania. It is led by Dr. Hogenesch, an ITMAT investigator who is also Associate Director of the PGFI, itself co-directed by ITMAT investigators Drs. Eberwine and Kim. Thus the structures and individuals focused on the informatics infrastructure of clinical and translational research are closely interwoven within ITMAT and in BIIT. The PCBI brings together faculty and researchers from across the university, housing laboratories and facilitating collaboration among diverse scientific disciplines.

PCBI’s objectives are to:

1. promote research collaborations between biologists, computer scientists, and mathematicians for the advancement of biomedical, as well as computational sciences;
2. educate the next generation of researchers and practitioners in the field of bioinformatics; and
3. develop and strengthen interactions between academic and industrial researchers to promote research in bioinformatics.

Educational programs have been established at the undergraduate, masters, and Ph.D. levels; a number of postdoctoral researchers are also supported to contribute to the research program and receive cross-training from the major field of interest. To foster closer collaboration with other academic institutions in the Philadelphia area, as well as with the pharmaceutical and biotech industries, the Penn Bioinformatics Forum (PBF) has also been established. PBF is a monthly seminar series open to the Penn, pharmaceutical, and biotech communities in the Philadelphia area, and provides a neutral location for people involved in bioinformatics to learn about recent advances from experts in the field, exchange ideas, and hold general discussions about issues of common concern.

CHOP Center for Biomedical Informatics (CBMi):

CBMi, initiated in February 2006, provides a structure for all research informatics activities at CHOP, including the development and deployment of intellectual, technical, educational and service-based resources in biomedical computing. CBMi encompasses existing service units for bioinformatics and clinical reporting from hospital systems; works closely with fast-tracked efforts to create a single electronic health record for all CHOP clinical activities; partners with existing CHOP-based groups for outcomes research, quality improvement, decision support, biostatistics, and bioethics; and closely coordinates the analysis of high-throughput genomic data derived from CHOP-based samples. CBMi includes nearly 20 affiliated faculty pursuing informatics academic research at CHOP, as well as a translational informatics group that explores and pilots novel informatics solutions for research CHOP-wide. CBMi also serves as the primary informatics interface with Penn, facilitated through BMIC.

Penn Clinical Care and Laboratory Medicine Enterprise:

The UPHS informatics personnel and computing resources are centralized within a highly- effective unit, led by CIO Michael Restuccia, who reports to Kevin Mahoney, Chief Administrative Officer and Vice-Dean for Integrative Services. In that capacity, both Mr. Mahoney and Mr. Restuccia have been strong advocates for aligning research IT across the health system and research enterprise. UPHS informatics supports the full range of health care-related services that require specialized Information Technology (IT) and Information Systems (IS) services. Pathology and Laboratory Medicine recently moved their clinical pathology informatics group into corporate IT under CIO Mike Restuccia to better synergize with the UPHS clinical mission. The governance model is that Laboratory IT reports to Mr. Rick Bryson who reports directly to the CIO. A nascent translational and computational group in pathology is being formed to support research projects.

PENN Biomedical Research Computing (BRC):

The BRC consists of 6 FTEs specializing in the architecture, development, and implementation of advanced IT infrastructures, designed to support the biostatistical and research informatics required on CTSA-sponsored biomedical and clinical research projects. The BRC ensures the integrity of the research computing services across all servers, databases, storage, and backup devices for projects and data within the BRC data/network domain.

The BRC “mission” is:

1. address high-end computational/statistical needs of biostatistics faculty, graduate students and post-doctoral fellows;
2. provide robust database platforms;
3. maintain data classification and storage paradigms (FISMA-compliant and secured);
4. provide business continuity and recovery; and
5. liaison with other Research computing groups in support of sponsored projects.
6. These services are absolutely essential for the successful conduct of a complex array of projects in meeting sponsor compliance requirements.

IT infrastructures supported by BRC include:

1. separate and secured network domains managed apart from other SOM data networks;
2. Identity and Access Management configurations used in conjunction with existing SOM/Penn domains to provide external user authentication;
3. authenticated and secured access to appropriate project data structures;
4. access to high-end computing grids/servers for statistical and programming requirements;
5. configuration, operations, and management of the network, compute servers, and access methods used for sponsored project work;
6. support for Oracle-specific portal, application, and document management servers;
7. management of sponsor/customer communities that reside outside of the University, but participate in the University’s research projects.

The BRC is currently further developing a new core configuration of infrastructure services and software to allow for CTSA research needs to “scale-out” incrementally by only adding resources on demand to service project-specific needs.

PENN Research Data Center:

Building on current strengths across the Penn Medicine research computing community, PENN has committed major new investments to enhance the research computing infrastructure, to include training core technical staff, extending high-speed/high volume connectivity and network transmission capacity to primary research groups throughout the campus, and promoting the centralization and consolidation of the various information technology (IT) resources within a “Research Data Center.”

This Research Data Center (RDC) provides the appropriate centralized computing facilities (single campus site) for research computing activities. The RDC is equipped with HVAC, multiple-staged power feeds via UPS and generator backups, fiber connectivity to Internet-2, as well as intra-campus fiber accessible to all primary research groups. RDC houses a growing array of compute/analysis and database servers, storage and back-up devices, including bioinformatics computing servers (e.g., clusters) and software (e.g., LIMS), specialized clinical research informatics (CRI) computing servers, e.g., high performance computing (HPC), and software, e.g., Oracle Clinical (OC), Velos, and REDCap; all enterprise applications used across the research computing community.

High volume imaging data and other high-throughput research data necessitate that the RDC be connected to high-performance data networks to provide network responsiveness. PENN manages the regional Internet2 GigaPoP (MAGPI). This high-performance network has connections to the Penn campus and the RDC, CHOP, and other regional research and educational institutions, providing several gigabyte-per-second connection points.

Core IT infrastructure services are provided by dedicated groups of research IT computing personnel. Services include server management and configurations, backup services, disaster recovery services, storage area data network (SAN) management, network security, as well as compliance and regulatory services for investigators. These centralized IT resources are also provided and services are available for smaller research groups that currently do not support their own IT personnel, but who have emerging needs for specialized computing equipment. In addition to the campus RDC, the research community also has access, and can utilize an off-campus Tier-3+ Data Center facility managed by CSC (under contract with Penn Medicine), which has IT infrastructure and computing capabilities to provide nearly unlimited virtual, physical, and private cloud computing capabilities.

Center for Biomedical Informatics in Translation (BMIC) Contacts

Richard Landis, PhD

Professor of Biostatistics and Statistics
Director, Division of Biostatistics, Department of Biostatistics & Epidemiology (DBE)
Director, Biostatistics Unit, Center for Clinical Epidemiology & Biostatistics (CCEB)
Faculty Co-Director, Clinical Research Computing Unit (CRCU)
Perelman School of Medicine at the University of Pennsylvania
600 Blockley Hall, 423 Guardian Drive
Philadelphia, PA 19104-6021
215-573-4922 (Office)
Email: jrlandis@mail.med.upenn.edu

Brian P. Wells, MBA, FHIMSS

Associate CIO Health Technology and Research Computing
Corporate Information Services
Penn Medicine
Corporate (UPHS) Information Services
3001 Market Street, Suite 400
Philadelphia, PA 19104
Tel: 215-614-1923
Email: brian.wells@uphs.upenn.edu

Michael D. Feldman, MD, PhD

Associate Professor of Pathology and Laboratory Medicine
Division of Surgical Pathology, 6 Founders
Hospital of the University of Pennsylvania
3400 Spruce Street
Philadelphia, PA 19104-6021
215-662-6503 (Office)
Email: feldmanm@mail.med.upenn.edu

Robert M. Curley, MS

Senior Director for Methodologies and Special Projects
Perelman School of Medicine at the University of Pennsylvania
Center for Clinical Epidemiology & Biostatistics
Clinical Research Computing Unit (CRCU)
3535 Market Street, Suite 560
Philadelphia, PA 19104-3309
215-573-7397 (Office)

James Kaylor, MSE, CISM

Senior Director, Information Services & Technologies
Perelman School of Medicine at the University of Pennsylvania
Center for Clinical Epidemiology & Biostatistics
Clinical Research Computing Unit (CRCU)
Biomedical Research Computing (BRC) Unit
3535 Market Street, Suite 560
Philadelphia, PA 19104-3309
215-898-2558 (Office)
215-573-6262 (Fax)
Email: jkaylor@mail.med.upenn.edu

Greg Grant, PhD

Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
Perelman School of Medicine at the University of Pennsylvania
806 BRB II/III, 421 Curie Blvd.
Philadelphia, PA 19104-6160
215-573-3736 (Office)
Email: ggrant@pcbi.upenn.edu

Peter White, PhD

Research Associate Professor of Pediatrics
Director, Center for Biomedical Informatics
3535 Market St. Room 1407
Philadelphia, PA 19104
215-590-5241 (Office)
215-590-5245 (fax)
Email: white@genome.chop.edu Assistant: Shana Goldson
267-426-0670 (Office)
215-590-5245 (fax)
Email: goldson@genome.chop.edu

Chris Forrest, MD, PhD

Senior Vice President, Chief Transformation Officer
34th & Civic Center Boulevard
Abramson Research Center bldg. Room 1335
Philadelphia, PA 19104
267-426-6917 (Office)
267-426-6995 (fax)
Email: forrestc@email.chop.edu
Assistant: Sue Lawerance
267-426-6907 (Office)
267-426-6995 (fax)
Email: lawrence@email.chop.edu

John Matthews, J.T., RRT MBA

Clinical Trials Office
34th & Civic Center Boulevard Main Hospital A-230
Philadelphia, PA 19104
215-590-0118 (Office)
215-590-31022 (fax)
Email: matthewsj@email.chop.edu

Ge Zhang, PhD

Director of Bioinformatics Core
3535 Market St. Room 1408
Philadelphia, PA 19104
267-426-7172 (Office)
215-590-5245 (fax)
Email: zhang@genome.chop.edu

Robert Grundmeier, MD

Attending Physician
3535 Market St. Suite 1380
Philadelphia, PA 19104
Email: Grundmeier@email.chop.edu
Assistant: Kelli Moore-Dolison
215-590-2857 (Office)
267-426-2455 (fax)
Email: dolison@email.chop.edu

Peter Witzleb

Director, Research Information Services
34th & Civic Center Boulevard
Abramson Research Center, Suite 313
267-426-2707 (Office)
Email: witzleb@email.chop.edu

Responses to COVID-19

The informatics group have been intensely involved at local and national levels as we prepare for the surge of cases of COVID-19. We have created a comprehensive REDcap based questionnaire and are collaborating with CD2H to share this resource, harmonize our collection of biosamples and store the data in the cloud. We will integrate this information with EHR linked data and go to scale through the Accelerated Trials Network to identify factors in that predict the clinical course of asymptomatic infected patients so better to allocate resources and design preventative trials. Finally, we have deployed W2H in collaboration with Google to facilitate remote consenting, patient management and communication.