%0 Journal Article
%T Yabi: An online research environment for grid, high performance and cloud computing
%A Adam A Hunter
%A Andrew B Macgregor
%A Tamas O Szabo
%A Crispin A Wellington
%A Matthew I Bellgard
%J Source Code for Biology and Medicine
%D 2012
%I BioMed Central
%R 10.1186/1751-0473-7-1
%X In this paper, we describe the architecture of a software system that is adaptable to a range of both pluggable execution and data backends in an open source implementation called Yabi. Enabling seamless and transparent access to heterogenous HPC environments at its core, Yabi then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. Yabi can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts. In this paper, we highlight Yabi's capabilities through a range of bioinformatics use cases that arise from large-scale biomedical data analysis.The Yabi system encapsulates considered design of both execution and data models, while abstracting technical details away from users who are not skilled in HPC and providing an intuitive drag-and-drop scalable web-based workflow environment where the same tools can also be accessed via a command line. Yabi is currently in use and deployed at multiple institutions and is available at http://ccg.murdoch.edu.au/yabi webcite.Chaining a number of analysis tools together to form domain-specific analysis pipelines or workflows is essential in many scientific disciplines [1-3]. For some scientists access to a command line login is all that is required for them to write custom scripts and programs to link these tasks. For instance, workflows can be
%K Bioinformatics
%K workflows
%K Internet
%K high performance computing
%U http://www.scfbm.org/content/7/1/1