Center for BioMedical Informatics Core (BMIC) Resources

Navigate Center for BioMedical Informatics Core (BMIC)

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:

  1. data resource needs assessment;
  2. evaluation, selection and deployment of commercial software tools (eg, REDCap, Velos, Oracle Clinical);
  3. development of specialized software systems;
  4. support for data collection, management, and integration;
  5. guidance on computing hardware support and
  6. 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 IBI Bioinformatics Core (BIC):

The IBI Bioinformatics Core is led by Dr. Taehyong Kim (Director) and Dr. Li Shen (Faculty Director), and provides professional bioinformatics services, including data analysis and consultation to the Penn biomedical research community. The core is also dedicated to build efficient pipelines to handle various next-generation sequencing (NGS) data including RNAseq, DNAseq, ChIPseq and single cell analyses with in-house NGS pipelines as well as publicly available tools and platforms.

The Bioinformatics Core is also supported by IBI faculty members whose areas of expertise include NGS-related algorithm development, human disease research (diabetes, cancer, Autism, Alzheimer’s disease etc.), functional genomics, statistical genetics, and computational biology. We provide bioinformatics support for grant applications in all biomedical areas by reviewing informatics approaches, offering computation resources and expertise for the proposed research.

Penn IBI Clinical Research Informatics Core (CIC):

The Clinical Research Informatics Core (CIC) of the Institute for Biomedical Informatics (IBI) is led by Dr. Danielle Mowery, and provides an array of computational services to support the utilization of clinical data for biomedical research at the University of Pennsylvania. The CIC also provides assistance with clinical data access, machine learning, natural language processing, and data visualization.

Penn IBI Artificial Intelligence Collaboratory:

The IBI Artificial Intelligence Collaboratory is a group of Penn informatics faculty with expertise in artificial intelligence, data mining, machine learning, natural language processing, pattern recognition, and text mining who are interested in collaborating on biomedical and clinical research projects. The goal of this collaboratory to help the biomedical research community identify collaborators with expertise in artificial intelligence, machine learning, natural language processing, and other related areas.

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 (CHOP link); 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.

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.