Welcome

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 If you see information that looks out of date please don't hesitate to ask about it or fix it.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 support.

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
• 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. 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.

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, technology that 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.

Outreach

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), Heflin Genomics Center, the Comprehensive Cancer Center (CCC), the Department of Computer and Information Sciences (CIS), the Department of Mechanical Engineering (ME), Lister Hill Library, the School of Optometry's Center for the Development of Functional Imaging, and Health System Information Services (HSIS).

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 self-service installation documentation and supports using MATLAB on the HPC platform, providing a pathway to expand your computational power and freeing your laptop from serving as a compute platform.

UAB MATLAB Information In January 2011, UAB acquired a site license from Mathworks for MATLAB, SimuLink and 42 Toolboxes. Learn more about MATLAB and how you can use it at UAB Learn more about the UAB Mathworks Site license and review frequently asked questions about the license

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 support for more information or follow the links below.

Galaxy A web front end to run analyses on the cluster fabric. Currently focused on NGS (Next Generation Sequencing; biology) analysis support. Galaxy Project Home Galaxy Development Wiki UAB galaxy-dev list server

The Advanced Technology Lab (a.k.a. @lab) is the technology testbed for the Research Computing Group. We are developing a suite of applications to facilitate the research process. We use the RCS for our own research and development activities, building applications to share with others. We eat our own dog food.

One of our main applications is the Research Notebook, designed to help integrate services on the RCS into research operations.

Research Notebook This wiki also hosts the ResearchNotebook and the ResearchArchive wiki. The ResearchNotebook provide a commons to discuss academic research and academic writing at UAB. The ResearchArchive was a pilot repository to demonstrate hosting primary data, presentations, ePrints, and other products of the 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.