Neptune is a research data warehouse that has been established to provide electronic medical record data for research data marts and for clinical and translational research. Neptune consists of four major components that include 1) an operational data store, 2) an atomic data store, 3) a map store, and 4) an integrated view.


This work is funded by grant UL1 TR001857 from NCATS, NIH.



REDCap is a mature, secure web application for building and managing online surveys and databases. Using REDCap’s stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a ‘data dictionary’ template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods.

This work is funded by grant UL1-TR-001857 from NIH.




The Biomedical Informatics Core of the Clinical and Translational Science Institute (CTSI) will establish a research data warehouse; develop and deploy user-friendly, web-based informatics tools such as a Cohort Discovery Tool, a Computable Phenotype Library, and a Data Transfer Tool; and develop and deploy a secure data analytic environment.


This work is funded by grant UL1 TR001857 from NCATS, NIH.



Health Record Research Request (R3) is a service of the Department of Biomedical Informatics (DBMI) managed by the Chief Research Informatics Officer (CRIO), sponsored in part by the Clinical and Translational Sciences Institute and Institute for Precision Medicine. Pitt and UPMC desire to make clinical data available for research. Under the CRIO, on behalf of UPMC, DBMI staff provision data for research (in some cases as Honest Brokers) primarily via our Research Data Warehouse, Neptune. R3 is this service or process of provisioning UPMC clinical data and of authorizing additional UPMC data sources for research. R3 is available for use by researchers of the University of Pittsburgh, and for UPMC projects requiring research datasets. To engage R3 please use the R3 Intake Form (less than 30 seconds to fill out including principal investigator contact information and pasting in a brief project description). R3 team can be contacted with any questions at

More Information:

Download The R3 Introduction PowerPoint

Download and Play the R3 Introduction PowerPoint (Audio) 

Publications Using Health Record Research Request (R3) Service

Genomics Analysis Core


The aims of the Genomics Analysis Core (GAC) are to:

  1. provide genomics data analysis with emphasis on rigor and reproducibility
  2. provide genomics education
  3. partner with Center for Research Computing (CRC) and Pittsburgh Supercomputing Center (PSC) to develop computing infrastructure
  4. support team science projects.

The GAC provides support for all aspects of translational studies – from experimental design to data analysis to publication.  The GAC works closely with the Health Science Library System Mol Bio Service, and the Center for Research Computing, in directing researchers appropriate resource for genomics education, analysis and computing.


  • Bioinformatic Data Analysis
  • Genomics Education
  • High Throughput Computing
  • Team Science Projects

Cancer Bioinformatics Services


Cancer Bioinformatics Services (CBS) provides comprehensive bioinformatics support for translational genomics at UPMC Hillman Cancer Center. CBS provides support for all aspects of genomics studies, from experimental design to data analysis to publication, and for all genomic Next Generation Sequencing (NGS) applications, including RNA Seq, WES, WGS, ATAC Seq, single cell RNA Seq, immunogenomics profiling, neoantigen prediction, microbiome 16S rRNA-gene amplicon and metagenomics shotgun sequencing. CBS also works closely with the computing resources such as the Pittsburgh Supercomputing Center (PSC) and the University of Pittsburgh’s Center for Research Computing (CRC). CBS teaches genomics classes at the Health Science Library System (HSLC) and CRC. CBS supports small projects to larger team science projects such as the Big Data to Knowledge (BD2K), PACURE’s Big Data for Better Health (BD4BH), Breast Cancer Research Foundations AURORA project on metastatic breast cancer and HCC’s SPORE programs.