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Attention: Research Computing Documentation has Moved

Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.

As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

Welcome to the Research Computing System

The Research Computing System (RCS) is a private cloud supporting researchers at UAB.

The Research Computing System provides a framework for sharing data, accessing compute power, and collaborating with peers on campus and around the globe. Our goal is to construct a dynamic "network of services" that you can use to organize your data, study it, and share outcomes.

'docs' (the service you are looking at while reading this text) is one of a set of core services, or libraries, available for you to organize information you gather. Docs is a wiki, an online editor to collaboratively write and share documentation. (Wiki is a Hawaiian term meaning fast.) You can learn more about docs on the page UnderstandingDocs. The docs wiki is filled with pages that document the many different services and applications available on the Research Computing System. If you see information that looks out of date please don't hesitate to ask about it or fix it. If you want to create your own wiki for your lab or research project please contact [1].

The Research Computing System is designed to provide services to researchers in three core areas:

  • Data Analysis - using the High Performance Computing (HPC) fabric we call Cheaha for analyzing data and running simulations. Many applications are already available or you can install your own
  • Data Sharing - supporting the trusted exchange of information using virtual data containers to spark new ideas (available beginning September 2012)
  • Application Development - providing virtual machines and web-hosted development tools empowering you to serve others with your research

Support and Development

The Research Computing System is developed and supported by UAB IT's Research Computing Group. We are also developing a core set of applications to help you to easily incorporate our services into your research processes and this documentation collection to help you leverage the resources already available.

The Research Computing System is an out growth of the UABgrid pilot, launched in September 2007 which has focused on demonstrating the utility of unlimited analysis, storage, and application for research. RCS is being built on the same technology foundations used by major cloud vendors and decades of distributed systems computing research that has powered the last ten years of large scale systems serving prominent national and international initiatives like caBIG, the Open Science Grid, TeraGrid, and the LHC Computing Grid.


The UAB IT Research Computing Group has collaborated with a number of prominent research projects at UAB to identify use cases and develop the requirements for the RCS. Our collaborators include the Center for Clinical and Translational Science (CCTS), the Comprehensive Cancer Center (CCC), the Department of Computer and Information Sciences (CIS), the Department of Mechanical Engineering (ME), and Health System Information Services (HSIS).

We follow the best practices of the Open Source community and develop the RCS openly. You can follow our progress via the our development wiki.

As part of the process of building this research computing platform, the UAB IT Research Computing Group has hosted an annual campus symposium on research computing and cyber-infrastructure (CI) developments and accomplishments. Starting as CyberInfrastructure (CI) Days in 2007, the name was changed to UAB Research Computing Day in 2011 to reflect the broader mission to support research. IT Research Computing also participates in other campus wide symposiums including UAB Research Core Day in 2010 and UAB Research Core Day 2011.

Featured Research Applications

The Research Computing Group also helps support the campus MATLAB license with installation documentation and the ability to use MATLAB on our HPC resources to expand your computational power and free computing resources on your laptop or in your lab.

UAB MATLAB Information

In January 2011, UAB acquired a site license from Mathworks for MATLAB, SimuLink and 42 Toolboxes.

The UAB IT Research Computing group, the CCTS BMI, and Heflin Center for Genomic Science have teamed up to help improve genomic research at UAB. Researchers can work with the scientists and research experts to produce a research pipeline from sequencing, to analysis, to publication. Please contact [2] for more information or follow the links below.


A web front end to run analyses on the cluster fabric. Currently focused on NGS (Next Generation Sequencing; biology) analysis support.

The Advanced Technology Lab, the technology testbed for the Research Computing Group, is also developing a suite of applications to facilitate the research process. We use the RCS for our own research activities and to build new applications to share with others. We eat our own dog food. One of our leading applications is the Research Notebook, designed to help integrate these resources into custom research workflows.

Research Notebook

This wiki also hosts the ResearchNotebook and the ResearchArchive wiki. The ResearchNotebook provides a commons to discuss academic research and academic writing at UAB. It is the sister website for the Research Notebook blog [3]. The ResearchArchive is a pilot repository for primary data, presentations, ePrints, and other products of research effort at UAB. These projects are a collaboration between Lister Hill Library, UAB IT, and the School of Optometry's Center for the Development of Functional Imaging.