Informatics Resources

Secure Data Hosting


  • Provide UCSF research teams with a professionally managed, secure, web based, collaborative environment in which to store files containing sensitive data.
  • Provide application and data base services that allow investigators to view, manipulate, and save their data entirely in this protected environment without requiring files to be stored on their own computers.
  • Learn more! View a MyResearch Demonstration.
  • For more information contact
  • MyResearch Request Form (or email

Find and Share Datasets

Clinical Data Research Consultations

  • Clinical Data Research Consultations (formerly THREDS and IDR Data Extraction Service) is a service that extracts identified and de-identified patient data sets from UCSF Medical Center and San Francisco General Hospital (SFGH) hospital data sources for research purposes.
  • Request help with the development of custom REDCap forms, surveys, plugins, and hooks, and data management.
  • Typical uses of Clinical Data Research Consultations data include:
    • Summary statistics
    • Generation of condition-specific patient populations for study recruitment/chart review
    • Outcomes research using historical data in CHN databases
  • Clinical Data Research Consultations are provided by Academic Research Systems Service Now. The first 8 hours of service per Principal Investigator are complimentary each fiscal year. Submit a request
  • For more information contact

Research Data Browser (RDB)

  • This workbench enables researchers to browse, visualize, and export de-identified APeX patient data sets in a self-serve manner. Search records, export the summary or detailed data to Excel or CSV flat files for patient demographics, encounters, diagnosis, medications, labs, procedures. The RDB accesses UCSF clinical data since June 2012 without patient identifiers.
  • The RDB is for UCSF Staff, Faculty and affiliates only. To access you must be on campus or using VPN.
  • To request access please complete the Cohort Selection Tool and UC ReX Data Explorer Research Data Tools Request Form (requires MyAccess).
  • Learn more

UC ReX – University of California Research Exchange

  • Self-service search to explore patient population counts across the five UC Medical Center patient data sets to facilitate the potential identification of collaborators for cross-UC research studies. Once collaborators have been identified, a data extraction service is available to obtain de-identified and identified data sets for cohort identification and recruitment and retrospective data analysis.
  • To request access please complete the Cohort Selection Tool and UC ReX Data Explorer Research Data Tools Request Form (requires MyAccess).
  • Log in, query the data, fine tune queries as needed. When/if sufficient size of a cohort is found, contact the respective UC to get IRB approval to re-identify data.
  • More information

Comparative Effectiveness Large Dataset Analysis Core (CELDAC)

  • Data repository infrastructure for accelerated access to and use of local and national health datasets — View Dataset Inventory
  • Provides information on how to Work with Large Datasets
  • Provides guidance on Online Browsable Datasets
  • Supports studies assessing comparative effectiveness of clinical interventions
  • Consultation services provide expertise in statistics and use of large data sets to conduct comparative effectiveness and other T2 translational research
  • Request consultation


  • Share and download research datasets

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Collect & Manage Clinical Data

Research Electronic Data Capture (REDCap)

Data Management Consultation

  • For questions about how to design databases and workflow to support studies, and for assistance with actual programming of a variety of database.
  • Help with large national databases
  • Support and enhancement of Common Data Infrastructure (CDI) applications
  • Service provided via CTSI Consultation Request

Data Sharing & Data Management Guide

Qualtrics Survey Tool

  • Qualtrics allows faculty, researchers, staff and trainees to build, distribute, analyze and collaborate on complex surveys.

San Francisco Coordinating Center

  • The SF Coordinating Center specializes in coordinating multi-center studies in women's health, aging, cognitive function, cardiovascular disease, breast cancer prevention, osteoporosis, arthritis, and dementia. It uniquely combines scientific expertise in these areas with broad experience in managing multi-center studies, and offers access to our network of high quality, experienced clinical centers.
  • Contact: Chantelle Thomas

Translational Informatics

    • OnCore - The Online Collaborative Research Environment contains proprietary information pertaining to clinical trials, biospecimen studies, and patient registries. All patient information contained in OnCore is strictly confidential. Learn about OnCore training
    • Other services include free research planning consultation, data management, informatics grant writing support, i2e natural language processing system, Translational Informatics Penguin Compute Cluster (TIPCC), and more.

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'Omics Data

Bioinformatics Data Analysis

  • Provides consultation and assistance with analysis for data deriving from genomics, proteomics, microarrays, sequence and other high throughput biotechnologies.
  • Service provided via CTSI Consultation Request

Functional Genomics Core Laboratories

  • Provides expertise in experimental design, sample processing, hybridization and scanning, and data analysis.
  • To initiate a project, submit a project description form

Library Bioinformatics Support

  • Get access to and training on various biomedical data and software tools.

Preclinical Data

RIO (Research Information Online)

  • RIO is a comprehensive database management system that will link and store your research protocols, authorized users, online training programs and pertinent data. The goal of RIO is to facilitate quick turnaround times on complex processes and provide data integrity.



  • This virtual research desktop is loaded with research software and data storage and collaboration tools. MyResearch offers research software applications, such as SAS, Stata, SPSS, R, TreeAge, Atlas.ti, MS Office, and Matlab free of charge.
  • MyResearch also offers collaborative tools, such as SharePoint and the UC ReX Data Explorer, to facilitate the conduct of multi-site research studies.

Research Software Licensing (RSL)

  • Research Software Licensing offers annual licenses for research software to UCSF faculty and staff.
  • Contact: RSL Help, 415-476-4389

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UCSF Training Opportunities

Library Classes

Learn about bioinformatics resources available to the UCSF community, including databases and analytical tools. Check the class schedule for more information

Graduate Programs

The UCSF Graduate Program in Biomedical and Medical Informatics offers PhD training:

  • The Bioinformatics pathway provides multidisciplinary graduate study in biological composition, structure, function and evolution at the molecular and systems levels. Bioinformatics relies on techniques from applied mathematics, informatics, statistics, computer science, physics, chemistry, and biology to study biological composition, structure, function, and evolution at the molecular, cellular, and systems levels. It comprises all aspects of the gathering, storing, analyzing, predicting, and disseminating the corresponding information.

    Contact: Julia Molla, Bioinformatics Program Administrator, 415-514 0249

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External Resources

Professional Informatics Organizations

Funding Opportunities

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