Informatics Resources

Secure Data Hosting

MyResearch@UCSF

  • Provide UCSF research teams with a professionally managed, secure, web based, collaborative environment in which to store files containing sensitive data. Read more about secure data hosting.
  • 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 its-arssupport@ucsf.edu
  • MyResarch Request Form (or email arsmyresearchsupport@ucsf.edu)

Find and Share Datasets

Integrated Data Repository (IDR)

  • A secure, convenient and compliant data warehouse of clinical and life sciences data for use by researchers. The IDR is a multi-year project supporting cohort scanning, hypothesis testing, correlative studies, and retrospective analysis of well-defined populations. It currently includes a de-identified copy of the UCSF Medical Center APeX demographics, procedures, vital signs, medications, labs, and diagnoses data sets. More data sets are planned, including UCSF School of Dentistry Axium data set and the San Francisco General Hospital Lifetime Clinical Record hospital data set.
  • IDR is part of the Clinical Data Research Consultations (CDRC) Data Extraction Service which provides identified, de-identified, and aggregate patient data sets, free to the UCSF research community. Submit a request for CDRC data extraction
  • Extracted for each request will be delivered into the requestor's MyResearch account, see below.
  • For more information contact its-arssupport@ucsf.edu

Research Data Browser (RDB)

  • The RDB is a web-based tool that allows researchers to explore UCSF EHR (APeX) data in a self-serve manner. Search de-identified patient clinical 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.
  • Find instructions for gaining access, training materials, and more information

UC ReX – University of California Research Exchange

  • Self-service search to get counts of potential patients for a study. Enable search of 12 million de-identified patient records from UC Davis, UC Irvine, UCLA, UC San Diego, and UCSF.
  • To request access please complete the Cohort Selection Tool and UC ReX Data Explorer Account 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

Clinical Data Research Consultations

  • Clinical Data Research Consultations (formerly THREDS and IDR Data Extraction Service) is a service that extracts data sets from UCSF Medical Center and San Francisco General Hospital (SFGH) hospital data sources for research purposes.
  • 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. Submit a request
  • For more information contact its-arssupport@ucsf.edu

DataShare

  • 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

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.
  • Other services include free research planning consultation, Vision Tree Optimal Care (VTOC), i2e natural language processing system, 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.

Software

Research Software Licensing (RSL)

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

UCSF Policy on Income Distribution for Unpatented Software

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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.

    Director: Tom Ferrin, PhD
    Contact: Julia Molla, Bioinformatics Program Coordinator, 415-514 0249

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External Resources

Professional Informatics Organizations

Funding Opportunities

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