Clinical & Research IT (Draft)

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John Kerrigan, PhD, and Manish Parashar, PhD 

Planning and implementation of a robust clinical data warehouse and data mining and discovery tools to support Precision Medicine applications including development of interfaces to pathology reports, electronic patient records, collaborators and vendors. Maintaining collaborator and vendor relationships. Developing processes and workflows.

Warehouse Services/Integrative Cancer Biology and Data Mining
Biomedical research has yet to fully harness the transformative power of information technology to enhance research productivity and efficiency, which accelerates research discoveries that transform clinical practice. Effective aggregation and management of knowledge along with data resources is critical to advancing clinical and translational science. It is a priority of the Biomedical Informatics Shared Resource to organize and implement informatics initiatives and their associated cyber-infrastructure and support capabilities to meet these needs. A major component of the efforts in support of integrative cancer biology is focused on developing, deploying and supporting data repositories using commercial and/or open source software that meet the specific requirements of Rutgers Cancer Institute members.  The Clinical & Research IT team is managing LabMatrix (BioFortis, Columbia, MD) a web-accessible clinical & translational research management software system used for information management and integration of patient, clinical, specimen, genetic and molecular assay data. Data repositories will provide federated access to clinical data, archive research datasets from completed studies, link research data sources for multidisciplinary collaboration, and serve as a platform for translational research. Targeted clinical data sources for phase I of the project include the ARIA-EMR containing encounter, laboratory, other EMR data, computerized physician order entry and data originating from radiology reports, pathology reports, surgical notes, clinical history, nursing notes, genomic sequencing studies, and information resident in OnCcore which supports ongoing clinical trials. Examples of research data sources that will be integrated into the data warehouse in phase II of the project include radiology PACS, digitized pathology repositories, and epidemiologic data from Rutgers Cancer Institute Shared Resources, NJ State Cancer Registry/SEER and databases linking Rutgers Cancer Institute’s Network of Hospitals, etc. As part of data repository development, wherever possible, the Biomedical Informatics Shared Resource is implementing a standard format to which data from heterogeneous sources will be transformed for further use. Standardization will facilitate data sharing both within and outside Rutgers Cancer Institute. The data structures within repositories are searchable and graphically browsable with data elements, volume and date range of the source, as well as standard and lexical reference to the data element (such as DICOM, HL7 v2.x, SNOMED, UMLS, caDSR, ICD10) where applicable.

Clinical Data Repository and Services
There is a need for a data repository for the population sciences, epidemiologists and clinicians in the various disease specific groups at Rutgers Cancer Institute to view populations and disease trends of patients. To support phase I studies and NCI-investigator driven clinical trials at Rutgers Cancer Institute, the Biomedical Informatics Shared Resource works with Rutgers Cancer Institute’s Office of Human Research Services in providing hardware, software and disaster recovery support for the OnCore Clinical Trial Data Management System. They are working with the commercial vendor to expand on the capabilities for real-time electronic data capture from our Aria-EMR as well as expanding on the OnCore Biospecimen Module that will facilitate integration with the data capture efforts in our Biospecimen Repository Service Shared Resource. The Biomedical Informatics Shared Resource ensures that the right data in the right format flows into appropriate data repositories in an efficient and secure manner. They have supported the Rutgers Cancer Institute membership using CAISIS (see, which is an open source, web-based, cancer data management system that integrates research with patient care. CAISIS was developed by Memorial Sloan-Kettering Cancer Center and is now utilized by many of the Comprehensive Cancer Centers for their own research as well as for the exchange of data to create larger populations and cohorts for study.

Rutgers Discovery Informatics Institute (RDI2) 
(RDI2) ( was created in 2012 as New Jersey's Center for Advanced Computation, an institute with the overarching goal of establishing a comprehensive and internationally competitive Computational and Data-Enabled Science and Engineering (CDS&E) effort at Rutgers University that will nurture the fundamental integration of research, education, and infrastructure.

RDI2 also hosts the Cloud and Autonomic Computing Center (CAC), a national research center that was established in January 2008 between Rutgers University, The University of Florida, and The University of Arizona.  The overall goal of the center is to combine resources from these universities, private companies, and federal government to make all kinds of computer systems and applications -- from desktop computers to complex air traffic control systems and scientific and engineering applications -- more reliable, more secure, and more efficient.

Rutgers Discovery Informatics Institute is tightly integrated with Rutgers Cancer Institute of New Jersey with Dr. Parashar serving as Director of RDI2 and Associate Director of Research IT at the Biomedical Informatics Shared Resource at RCINJ and Dr. Foran serving as Director of Biomedical Informatics at RCINJ and Associate Director for Research Medical and Health Informatics at RDI2. As a result of this strong collaborative relationship RDI2  provides persistent high-performance computing and cloud support for several key computational imaging services and longitudinal tumor studies that are invoked from the Biomedical Informatics Shared Resources at Rutgers Cancer Institute.

The CAC center was funded by the Industry/University Cooperative Research Center program of the National Science Foundation, by its members from industry and government, and by university matching funds. CAC members are afforded access to leading edge developments in autonomic computing and to knowledge accumulated by academic researchers and other industry partners. Per NSF guidelines, industry and government contributions in the form of annual CAC memberships, coupled with baseline funds from NSF and university matching funds, directly support the Center's expenses for personnel, equipment, travel, and supplies.

RDI2 provides the Rutgers community with advanced computational resources as well as support, training and consulting services. Details can be found at

Support of Other Rutgers Cancer Institute of New Jersey Shared Resources 

The Biomedical Informatics Shared Resource develops the web portals for access to the services of other Rutgers Cancer Institute of New Jersey Shared Resources.  In addition, more specific Biomedical Informatics needs of various Shared Resources are met, as follows:

Biometrics Shared Resource

Weichung Joe Shih, PhD

The Biomedical Informatics Shared Resource provides:

  • Software engineering support and web portal development and maintenance
  • System administration support to maintain system and application software and trouble shoot desktop workstations used for statistical analysis by the Biometrics Shared Resource; and
  • High performance computing resources and scientific computing expertise on multi-core massively parallel supercomputers.

Functional Genomics Shared Resource

Shridar Ganesan, MD, PhD

The Biomedical Informatics Shared Resource deploys scalable, efficient and secure storage and archiving capabilities to ensure seamless flow from data acquisition to storage and processing. This involves increasing the existing computing resources within the Biomedical Informatics Shared Resource to meet immediate needs (currently 30TB and projected to grow to 100TB within a year). Based on the anticipated growth in storage needs and the costs involved in deploying and maintaining an in-house solution, we are also exploring new avenues (i.e. based on Cloud Computing) as a cost-efficient, financially and operationally viable option. The Biomedical Informatics Shared Resource also provides data analysis for users of the Functional Genomics Resource.

Biospecimen Repository Service Shared Resource

Lorna Rodriguez, MD, PhD

The availability of annotated specimens is enhanced by leveraging data available from our new EMR as well as from the NJ State Tumor Registry (NJSTR).

Histopathology Shared Resource

Lauri Goodell, MD

David Foran, PhD

The Biomedical Informatics Shared Resource provides cyber-infrastructure advice and support for the Telepathology Project, linking instrumentation for remote viewing of organs for transplant within a facility located at the Robert Wood Johnson University Hospital. In addition, informatics and software engineering experts at Dr. Foran’s Bioimaging Center are using the Biomedical Informatics Shared Resource HPC resources located at the Rutgers Cancer Institute's data center for code development and large-scale simulations. The Biomedical Informatics Shared Resource is working in partnership with Dr. Foran’s team to develop a large-scale storage facility to support research needs in pathology informatics in general and the data generated by the tissue microarray service. The Biomedical Informatics Shared Resource will maintain the hardware, provide system administration support and will be responsible for data backup and disaster recovery of all pathology imaging data.

Office of Human Research Services

Tracie K. Saunders, RN, MS

The Biomedical Informatics Shared Resource provides cyber-infrastructure advice and support for the Oncore Clinical Trials Software, a caBIG compatible commercial CTMS system that supports the data collection/management and study protocols for Rutgers Cancer Institute’s clinical trials. In addition, Oncore includes a software module that supports the data management for Rutgers Cancer Institute’s Biospecimen Repository Service Shared Resource. Our Database Architect worked with the company (Forte Research Systems) and biorepository colleagues to migrate the data stored in a homemade Perl-based software into the Oracle-based OnCore module.  Our HPC supervisor worked with the company to migrate the entire OnCore application and legacy data to new hardware, in the process implementing a failover mechanism by reconfiguring the hardware so that two of the servers are located in our data center and the other two identical servers at the Robert Wood Johnson University Hospital Data Center (with appropriate tape backup for disaster recovery). This would ensure 24/7 availability of data to OHRS and minimize loss of data in case of hardware or network failure.

Epidemiology Services Shared Resource

Antoinette M. Stroup, PhD

The Biomedical Informatics Shared Resource provides the newly developing Epidemiology Services Shared Resource with infrastructure and design support for research tracking and analytical databases.  Specifically, in support of all ESC-run population-based investigations of cancer prevention, etiology, treatment and outcomes, the Biomedical Informatics Shared Resource houses and maintains an application server (SunFire x4140) equipped with 2X6-core Opteron cpus, 32GB of RAM and 4x146GB disks linked to a back-up application server; and a storage server with 18 terabytes of secure, encrypted storage linked to a duplicate back-up server.  The application server can be used for statistical analysis of data sets using R or SAS.  The storage server provides up to 18 terabytes of secure, encrypted storage as noted.  In addition, the developing Epidemiology Services Shared Resource has access to the Biomedical Informatics Shared Resource secure, encrypted web server for hosting various research projects/initiatives.  As new study-specific needs arise for data base design and access controls, the Biomedical Informatics Shared Resource works with Epidemiology Support Services staff to meet these needs and support ongoing work.

Website/Interface Services

It is difficult for many projects to separate web development (website) from medical/clinical informatics and database design/installation since all these applications are through a web portal requiring a “website/interface” with underlying database design, programming and linkage to informatics. While a majority of the web portals are used to support ongoing outreach and educational initiatives, a significant number are targeted to the collection and integration of data in support of research in population science and translational research where integration of data from the lab, clinic and population based studies will advance our research agenda in cancer prevention, control and survivorship. At a practical level, the resources and manpower devoted to developing and deploying web portals benefits our research agenda at Rutgers Cancer Institute as it helps to increase recruitment for clinical trials carried out at the center by making patients and clinicians aware of the ongoing trials. Examples of projects implemented and maintained by the Bioinformatics Shared Resource include the following:   


For more information or to request services, please contact:

John Kerrigan, PhD