Informatics Grant Text

Investigators are encouraged to use the following text for their grants. If you need grant text for a topic not listed below, please contact Diana Gumas.

Johns Hopkins University & Medicine

The Johns Hopkins University (JHU) is a private research university in Baltimore, MD, founded in 1876. Johns Hopkins is organized into ten divisions on campuses in Maryland and Washington, DC, with international centers in Italy, China, and Singapore. The two undergraduate divisions, the Krieger School of Arts and Sciences and the Whiting School of Engineering, are located on the Homewood campus in Baltimore’s Charles Village neighborhood. The medical school, nursing school, and Bloomberg School of Public Health are located on the Medical Institutions campus in East Baltimore. The university also consists of the Peabody Institute, APL, the Paul H. Nitze School of Advanced International Studies, the Carey Business School, and various other facilities. Johns Hopkins is the largest research university in the world, as measured by research funding. In fiscal 2014, the university received $2.242 billion in medical, science, and engineering R&D, according to the National Science Foundation. Of that funding, $1.95 billion was from federal research funding agencies.

Johns Hopkins School of Medicine, established in 1893 in Baltimore, MD, currently engages 2,700 full time and 1,250 part-time faculty. Training more than 1,250 medical and doctoral students annually, it is consistently ranked among the top three schools of medicine in the U.S. News & World Report’s Best Medical Schools listing. The Medical Institutions, located alongside the School of Public Health on JHU’s East Baltimore Campus, provide outstanding clinical and scientific resources and a rich environment for the conduct of patient-oriented research. One of the great strengths of Johns Hopkins is its culture as a multidisciplinary collaborative research community within a premier clinical and educational institution. The highly networked research environment will help to make it possible to successfully complete the proposed project. Hopkins retains an innovative spirit, annually receives more research grants from NIH than any other medical school, and consistently is ranked among the top two NIH-funded medical schools in the nation.

The ICTR Informatics and the Informatics Core

The Johns Hopkins Institute for Clinical and Translational Research (ICTR), established in 2007, is one of more than 60 medical research institutions working together as a national consortium to improve the way biomedical research is conducted across the country. The ICTR addresses obstacles in translating basic science discoveries into research in humans, translating clinical discoveries into the community and communicating experience from clinical practice back to researchers. The ICTR Informatics Core (i2c) provides multiple tools and services to assist clinical researchers with integrated study management. These tools and services include cohort feasibility assessment, study recruitment, a study participant registry, using Epic to collect data in a way that is integrated with the clinical workflow, data acquisition from institutional data sources, and tools for collecting study data outside of the Epic medical record when appropriate.

Data Access

The Core for Clinical Data Acquisition (CCDA) assists researchers with access to clinical data from PMAP, Epic, and legacy patient information systems. The CCDA works closely with the Data Trust Research Sub-council and the IRB, serving as an institutional honest broker. Our services include providing:

  1. Preliminary, anonymous data for feasibility, grant applications, and estimating sample sizes
  2. IRB-approved case-finding for study enrollment, chart review, and cohort/case-control studies
  3. One-time and ongoing periodic data extracts
  4. Natural Language Processing to analyze text documents and extract data from the text
  5. Data de-identification services
  6. Assistance using self-service tools such as Epic’s SlicerDicer
  7. Specialized study data collection services such as i2b2, and interfaces to REDCap
  8. SAFE Desktop, a secure data analytic environment

The CCDA is the trusted Johns Hopkins Data Trust honest broker for clinical data for research use and works closely with the Institutional Review Board. The CCDA staff includes a full time project manager, 5 Epic certified SQL data analysts, and a Natural Language Processing expert.

Program to Accelerate Clinical Research using Epic (PACE)

PACE was established to help clinical researchers take full advantage of the Epic Electronic Health Record system for their research projects. We provide guidance regarding existing Epic research functionality as well as designing and building customized Epic content for your project to enhance the efficiency and standardization of the data collection process and improve data quality. Potential applications of customized Epic build are numerous, and some typical scenarios include:

  1. Study recruitment using the Epic MyChart patient portal, with review and approval by the ICTR MyChart Epic-Based Recruitment team. https://ictr.johnshopkins.edu/programs_resources/programs-resources/research-participant-recruitment-and-retention/my-chartepic-based-recruitment/
  2. Alerts that identify specific patient subsets in the clinic setting. This may include alerts that a patient may qualify for a research study or that important clinical data are missing for a specific study participant.
  3. Tools that help providers collect discrete data on a population of interest. This may include documentation flowsheets and SmartForms as well as SmartSets that help populate Epic data fields in a standardized way. It may also include automatic calculation of patient scores based on multiple sources of data in Epic.
  4. Collection of patient-reported outcomes through the Epic MyChart patient portal and tablets in the waiting room.
  5. Tools that provide a comprehensive overview of the patient’s specific phenotype by pulling in relevant available data in Epic.
  6. Reports that aggregate and display data regarding a specific research study.

PACE encourages researchers to contact us at least a few weeks ahead of grant submission so that we may provide you with information about how you can use Epic for your research project, including an estimate for the cost to build new tools in Epic. The ICTR provides two complimentary hours of service per faculty to underwrite this activity. While the ICTR provides funding for an initial consultation for your proposal the subsequent Epic build, testing and maintenance is a fee for service program at a rate of $118/hour.

Other Institutional Resources

The Division of Health Sciences Informatics is the academic home in the School of Medicine for informatics researchers (mostly clinical and public health) and the PI. The Division has primary faculty as well as about 30 faculty with secondary appointments throughout the Schools of Medicine, Nursing, Public Health, Engineering, and elsewhere. These faculty have homes in the Center for Population Health IT, the Johns Hopkins Institute for Clinical and Translational Research, the Johns Hopkins Medicine Center for Information Services, and other units. Research includes information science (as in the case of the present proposal), computer science (decision modeling), clinical informatics (chronic-care solutions for the homebound), public health (population-based decision support), and others. The Division houses an active teaching program, with two master’s degree programs (Applied and Research), a post-baccalaureate certificate program, and a PhD program focused on clinical reengineering through informatics.

 

The Center for Inherited Disease Research (CIDR) within IGM provides high-quality genomic laboratory services along with statistical genetics consultation, data cleaning, imputation, reanalysis, and data deposition assistance to investigators working to discover genes that contribute to disease. CIDR’s overarching goal is to contribute to the identification of genes and variants responsible for human traits, especially those involved in common complex diseases. In aggregate, these disorders account for a major fraction of human mortality and morbidity and, accordingly, a large share of health care costs. The past 8 years have seen enormous success of Genome Wide Association Studies (GWAS) with elucidation of more than 17,000 single-nucleotide polymorphism (SNP)-trait associations.

 

The Johns Hopkins University Applied Physics Laboratory (APL) is a not-for-profit organization and one of the divisions of JHU. APL was established in 1942 to solve an urgent wartime problem in ship anti-aircraft defense. Success with that, and later efforts, established APL as a model for today’s University Affiliated Research Centers (UARCs) that serve the nation’s interest as trusted technical agents. Located in Laurel, MD, APL is a diverse organization with more than 400 active projects at any given time; more than 4,000 engineers, scientists, and technical support personnel; and more than 140 specialized facilities. APL is a leader in integrative, collaborative research and has a long history of working directly with end users and stakeholders at all levels of government. This is demonstrated in the multitude of APL-supported programs—specifically those with a focus in the areas of biomedical and systems biology work, such as the Revolutionizing Prosthetics program, bio-surveillance programs, systems biology, and health care systems interoperability.

APL’s strength is its capability to support the development of synergy for a diverse set of entities, as well as between government and industry by acting on behalf of our government sponsors. This is accomplished by leveraging the expertise of our scientists, engineers, and technical staff with that of our experienced subject-matter experts, to include health care providers, nurses, epidemiologists, and public health and clinical staff. The result is outcomes that represent the true and accurate needs of our government sponsors and stakeholders.

An important distinction is that APL is a UARC, a designation established by Congress and administered by the Department of Defense (DoD) Director of Defense Research and Engineering (DDR&E) office. As a UARC, APL serves as an “honest broker” for the government and is a long-term “trusted agent” for many government programs, allowing it to develop comprehensive knowledge of sponsor requirements as well as build and sustain long-term collaborations and partnerships.

Finally, APL brings to the table a systems engineering strategy of sprint capability development, which will be utilized for this pilot project. The sprint development process is a systems engineering strategy used for complex projects with multiple diverse end users and stakeholders. It helps to manage risk, ensures successful coordination for a multitude of project elements, and overlaps with both technical and human-centered disciplines such as research, human systems engineering, technical engineering, organizational studies, and project management.

 

The Johns Hopkins Berman Institute of Bioethics is the home for collaborative scholarship and teaching on the ethics of clinical practice, public health, and biomedical science at JHU. Since 1995, the Institute has worked with governmental agencies and nongovernmental and private-sector organizations to address and resolve ethical issues. It is one of the largest bioethics centers in the world, with a multidisciplinary faculty of more than 30 experts spanning the fields of philosophy, science, medicine, nursing, law, public health, and the social sciences. Pertinent to this application is the Institute’s deep experience with consenting models, and return of results information.

 

The Bloomberg School of Public Health is the oldest and largest school of public health in the world. It comprises 670 full-time and 709 part-time faculty, enrolling 2,243 students from 81 countries. It has 10 graduate degree programs and 10 major departments, including several that are relevant to this PMI Pilot proposal: Biostatistics; Health, Behavior and Society; and Health Policy and Management. The School receives 20% of all research funding awarded to the 50 accredited schools of public health and has been ranked #1 by U.S. News and World Report since 1994.

 

The McKusick-Nathans Institute of Genetic Medicine (IGM) is the focal point of human genetics at the School of Medicine and has a long and continuous history of clinical service, research prominence, and educational activity in all aspects of genetics and genomics. The IGM includes 40 primary faculty and 35 affiliated faculty along with approximately 350 members that include more than 100 trainees (predoctoral students, residents, and research postdoctoral fellows), 9 genetic counselors, and more than 150 staff. The objectives of the IGM are to focus and enhance the efforts of the many basic scientists and clinicians at Hopkins on discovery of genetic mechanisms of human disease and the application of those discoveries to disease prevention and treatment. The research activities of IGM scientists cover the broad horizon of genetics and genomics from genome biology and assembly, DNA/protein interactions and epigenomics, identification of genes and variants causing or contributing risk for rare monogenic and common complex genetic diseases, genome editing and related techniques to model genetic diseases in cells and organisms, development and evaluation of innovative therapies, and evaluation of the ethical legal and social implications of genetic research.

 

The Department of Computer Science at JHU is a diverse, collaborative, and intensely research-focused department. The faculty spans a broad spectrum of disciplines encompassing core computer science and several cross-disciplinary application areas, including computational biology and medicine; information security; machine learning and data intensive computing; robotics, vision, and graphics; speech and language processing; systems; and theory and programming languages. Computer Science collaborates within the Whiting School of Engineering, including the Department of Biomedical Engineering, and has had longstanding engagement with the School of Medicine and APL. For this PMI Pilot proposal, we will leverage their world-class expertise in information security.

 

Johns Hopkins Department of Biostatistics is the oldest academic department of statistical science in the United States and has long been considered one of the best. With a rich history of outstanding contributions in both research and education, the Department advances statistical and data science, makes discoveries that improve health and health sciences, and provides an innovative biostatistics education for those seeking to be conversant with concepts as well as for users and experts in the application and development of new methodology. Currently, the Department comprises 39 full-time faculty, 12 postdoctoral fellows, and 50 PhD and 24 master’s students. Research in the Department is organized into six dynamic Working Groups (WGs) of faculty, postdoctoral fellows, and students. Groups meet regularly in a variety of formats, including research-in-progress sessions, journal clubs, topical seminars, and working discussions. The WGs include population modeling methods, methods and applications in genomics, advanced technologies for imaging and wearable computing, and causal inference. The Department is home to the Coursera Data Science Specialization that has enrolled more than 3.5 million students worldwide. This and other Specializations all have special emphasis on data visualization and communication.

 

The Armstrong Institute for Patient Safety and Quality (AI) is composed of an interdisciplinary research team of physicians, nurses, industrial and systems engineers, human factors engineers and psychologists, sociologists, statisticians, epidemiologists, and health services researchers with faculty from the Johns Hopkins School of Medicine, Bloomberg School of Public Health, Johns Hopkins School of Nursing, Johns Hopkins Whiting School of Engineering, and Johns Hopkins Carey School of Business. AI has established an extensive collaborative network including the World Health Organization (WHO) World Alliance for Patient Safety (WAPS), and the Institute is currently working with approximately 30 state hospital associations to improve care. AI has deep expertise in human factors and cognitive engineering, human–computer interaction, usability evaluation, qualitative methods (i.e., focus groups, interviews), questionnaire development, validation, and deployment. The Institute harnesses the expertise not just of clinicians but also of professionals from a broad range of disciplines, including human factors and systems engineers, psychologists, sociologists, and others.

 

The Johns Hopkins Individualized Health Initiative (Hopkins inHealth) is a collaboration among three Johns Hopkins institutions: JHU, the Johns Hopkins Health System, and APL. Hopkins inHealth’s vision is that health promotion and care can be increasingly tailored to meet each patient’s circumstances and preferences. The Initiative integrates biomedical and data science research to better measure each individual’s health status and trajectory and to develop these discoveries into tools that can improve health practice at the Johns Hopkins Health System and beyond. Hopkins inHealth researchers integrate clinical, genetic, lifestyle, and other data sources, then create innovative data science tools intended to improve decision-making in the prevention and treatment of a range of conditions, including cancer, cardiovascular disease, autoimmune disorders, and infectious disease.

 

The Center for Population Health IT (CPHIT) is a first-of-its-kind interdisciplinary center at JHU, the vision of which is to make Johns Hopkins a global leader in population-centric Health IT (HIT) research and development. The Center focuses on improving the health and well-being of populations by advancing state-of-the-art Health IT and related Internet and mobile-based e-health tools within public and private health care organizations and systems. Pertinent to this PMI Pilot proposal, CPHIT has deep experience with access to and integration of claims data into population and cohort data.

 

Maryland Advanced Research Computing Center MARCC is a shared computing facility located on theBayview Campus of Johns Hopkins University and funded by a State of Maryland grant to Johns Hopkins University through IDIES. MARCC is jointly managed by Johns Hopkins University and the University of Maryland College Park. MARCC offices are located in the Bloomberg Building (Homewood campus) of Johns Hopkins University.The main cluster at MARCC has over 19,000 cores and a combined theoretical performance of over 900 TFLOPs. The compute nodes are a combination of Intel Haswell and Ivy Bridge processors and Nvidia K80 GPUS connected via FDR-14 Infiniband interconnects. It also features two types of storage: 2 PB Lustre (Terascala) and 15 PB ZFS/Linux. The standard compute nodes contain 2 Intel Xeon E5-2680v3 (Haswell) processors, with 12 cores and 128 GB DDR4, 2.5 GHz (Marked TDP frequency) or 2.1GHz AVX base frequency. Each node has a theoretical speed of 960 GFlop/s. The large memory nodes are Dell PowerEdge R920 servers with quad Intel “Ivy Bridge” Xeon E7-8857v2, (3.0GHz, 12 core, 30MB, 130W). Each ndoe has 1024 core, 2. GB RAM. The GPU nodes are Dell PowerEdge R730 servers with dual Intel Haswell Xeon E5-2680v3 (12 5 GHz, 120W), 128 GB of 2133 MHz DDR4 RAM. (AVX frequency: 2.1GHz) and two Nvidia K80s per node. The FDR-14 Infiniband topology is 2:1 with 56 gbps bandwidth. The lustre file system provides an aggregate bandwidth od 25 gbps (read) and 20 gbps (write).