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

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.