Yabi: A Cross -Omics Internet-Based Platform for Bioinformatics Workflows

Bioinformatics tools must be easy-to-use to enable -omics researchers to uptake available supercomputing data and compute infrastructure. These tools must cater for researchers that are non-HPC specialists and non-software programmers – the majority of potential life science researchers. The open source system Yabi is outlined. Yabi primarily enables seamless and transparent access to heterogeneous HPC and cloud resources and then builds an analysis workflow environment that can create and reuse workflows. Yabi is able to manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Researchers are able to either use the web-based environment to drag-and-drop tools to create sophisticated workflows or alternatively use the yabi-command-line, which is designed for users more comfortable writing scripts or for configuring external workflow environments. Unlike other workflow environments, Yabi enables system administrators to configure as well as manage running tools via a web-based environment and without the need to write/edit software programs/scripts.

Outlined in this presentation are workflows for both NGS QC and de novo genome/transcriptome assembly. In addition, Yabi’s features are further emphasised through the simple and direct access of a Cloud-based installation of QIIME (Quantitative Insights Into Microbial Ecology - www.qiime.org) for NGS Metagenomic Amplicon studies.

Yabi (and screencasts of workflows) may be found at: http://ccg.murdoch.edu.au/yabi/

Reference: Hunter A, Macgregor B, Szabo T, Wellington C and Bellgard MI, Yabi: An online research environment for Grid, High Performance and Cloud computing, Source Code for Biology and Medicine 2012, 7:1 doi:10.1186/1751-0473-7-1 Published: 15 February 2012.