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

Background: High throughput –omics technologies are rapidly advancing our understanding of a range of biological systems relevant to Biomedical and Agricultural Sciences.  The exponential increase in omics data is becoming a significant bottleneck at various levels. Here we developed a user-friendly platform capable of leveraging multiple heterogeneous supercomputing (HPC) resources to cope with the processing and analysis demands of ever increasing omics datasets.

Method: We present an overview of the architecture of a software system that is adaptable to a range of execution and data environments in an open source implementation called Yabi. Enabling seamless and transparent access to heterogeneous HPC environments at its core, Yabi provides an analysis workflow environment that can create and reuse workflows for a range of applications. New tools can be easily configured and managed through a web-based environment.

 Results: To highlight Yabi’s capabilities, we implemented and customized analysis workflows for genomics, transcriptomics, metagenomics, proteomics and metabolomics applications including quality assessment, de novo assembly and statistical analyses. Furthermore, we show that Yabi can also access Cloud-based resources. Yabi is available at http://ccg.murdoch.edu.au/yabi/.

Conclusion: 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 web-based workflow environment where the same tools can also be accessed via a command line. Yabi enables collaboration, data sharing and reuse of analysis workflows within and between geographically distributed groups.