Tools

  • i2b2

    What is i2b2?

    i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System. i2b2 was developed as a scalable informatics framework designed for translational research. i2b2 was designed primarily for cohort identification, allowing users to perform an enterprise-wide search on a de-identified repository of health information to determine the existence of a set of patients meeting certain inclusion or exclusion criteria.

    i2b2 allows researchers to determine feasibility of a study by identifying whether or not a sizable amount of patients exist with their study-specific criteria. 

    Access to clinical data through i2b2 involves several easy steps. After setting up their access, authorized users can obtain summary data sets (useful for finding aggregate population characteristics or for estimating the number of patients at UAB who might be eligible as subjects for a planned clinical study) and detailed data sets (useful for enrolling subjects in a study or to explore research questions using retrospective data). 

    Access i2b2

    Access to i2b2 is available to UAB personnel via BlazerID, but also requires validation of several other items. Detailed instructions can be found here.

    1. Successful completion of at least one of the following courses
             - HIPAA Privacy/Security Training
         - IRB Investigator 101 Initial Training
         - IRB Investigator 101 Continuing Ed

    2. Submit an i2b2 Access Request Form 
         Please note: If you are not a Principal Investigator, you will require supervisor approval. 

    3. Acknowledgement of Restriction on the Use of Limited Data Sets 
        - Log-on to the UAB Learning Management System
        - Search the catalog for "Acknowledgement of  Restrictions on the use of limited data sets" and enroll in this course
        (Note: This must be completed once a year.)

    4. Your access will be activated within 48 hours of receiving your request if all applicable requirements are complete. 

    Support Materials:
      - i2b2 Manual
      - i2b2 Frequently Asked Questions

    If you experience any difficulty please contact Matt Wyatt

  • U-BRITE

    What Is U-BRITE?

    U-BRITE (UAB Biomedical Research Information Technology Enhancement) assembles new and existing HIPAA-compliant, high-performance informatics tools to provide researchers with a means to better manage and analyze clinical and genomic data sets and implements a “translational research commons” to facilitate and enable interdisciplinary team science across geographical locations.

    Benefits

    • Access to clinical data from Clinical Data Repository to build cohorts

    • Access to genomic and other omics data from Omics Data Repository to perform detailed analytical characterizations

    • Provides self-service analysis to biologists via Jupyter Notebooks and other Analysis Gateway abstractions

    • Encourages participation in Jupyter Notebook, git, conda, and Docker ecosystems, which facilitate more reproducible research and team science

    • Brings clinical researchers in closer contact with data scientists, informatics architects, and computer programmers

    • Enables quick prototyping for new methods and tools

    • Enables sharing of complex data to bioinformaticians

    Visit the U-BRITE site.

  • Galaxy

    What is UAB Galaxy?

    UAB Galaxy platform for experimental biology and comparative genomics is designed to help you analyze multiple alignments, compare genomic annotations, profile metagenomic samples and more from your web browser. This platform is built on Galaxy, backed by the Cheaha compute cluster, and powered by UABgrid.

    The primary uses of UAB Galaxy are to provide a simple web interface for NGS (short read sequencing) analysis for genomic and transcriptomic datasets, using tools like BWA, Bowtie, Tophat and Cufflinks, as well as simple sequence manipulation via the EMBOSS toolkit. 

    How to Access UAB Galaxy

    All you need is a BlazerId and a web browser to run NGS analyses on the UAB cheaha cluster.

    UAB Galaxy website

  • REDCap

    What is REDCap?

    REDCap (Research Electronic Data Capture) is a secure, web-based application for building and managing online surveys and databases.REDCap has a great presence on world map as a research data collection tool. 

    REDCap has a great presence on world map as a research data collection tool: Developed by Vanderbilt University exclusively designed to support data capture for research studies. It Is part of a worldwide consortium - 1421  active institutional partners in 88 countries. More than 164,000 projects in production/development, and 224,000 users. For long term repeated data collecting studies, longitudinal project can be created which provides the ability to define events and data collection forms associated to each event.

    REDCap provides automated export procedures for seamless data downloads to Excel and common statistical packages (SPSS, SAS, Stata, R), as well as a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields.

  • National COVID-19 Data Access

    N3C is Open for Business. Learn How to Get Started.

    The National COVID Cohort Collaborative (N3C) has created a large, centralized data resource available to the research community to study COVID-19 at a scale and statistical power not possible within any single institution. N3C has assembled a standardized collection of clinical, laboratory and diagnostic data from hospital electronic health records and health care plans across the country for analysis within an accessible, cloud-based data enclave. Here is how you can get involved:

    The DUR and IRB approval letter can be submitted to N3C once the DUA is signed by the University. In the meantime, CCTS Partner Institutions are establishing the requisite Data Use Agreements with N3C. See list of institutions with active DUAs.

    *On July 29th, CCTS and the UAB Informatics Institute hosted an N3C workshop aimed at preparing researchers to utilize this data resource. Access those presentation slides here. Recording of the event is available on the CCTS Video Channel.

    Read more