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). 

To Access i2b2:

1. You will need to complete the access request form which can be found: Here
  -  Please note: Trainees, Staff or Students will require supervisor approval.

2. Learning Management System: 
  -   Log-on to the UAB Learning Management System
  -   Search the catelog for "i2b2" or "limited date sets" and take the course entitlted "Acknowledgement of Restrication on the Use of Limited Data Sets".
      (Note: This must be completed once a year.)
  -   Wait until the nest day for completion information to reach i2b2.
  -   HIPAA and IRB- Human subjects Protection training are also required.

3. Support Materials:
  - i2b2_manual.pdf
  -  i2b2_FAQ.pdf

4. Log on to i2b2

5. If you experince any difficulty please contact Matt Wyatt at mwyatt@uabmc.edu

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

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

2. UAB galaxy website: Direct link

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.

REDCap: Direct Link