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Yabi: An online research environment for grid, high performance and cloud computing.

Adam A Hunter¹, Andrew B Macgregor, Tamas O Szabo

¹Centre for Comparative Genomics, Murdoch, Western Australia, 6150. mbellgard@ccg.murdoch.edu.au.

Source Code for Biology and Medicine

|February 16, 2012

Summary

This summary is machine-generated.

Yabi is an open-source workflow system simplifying complex life science analyses on high-performance computing (HPC) resources. It offers a drag-and-drop interface and command-line access for managing data and tools across distributed environments.

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Area of Science:

Life Sciences
Bioinformatics
Computational Biology

Background:

Significant demand exists for robust pipelines in life sciences to chain complex analysis tasks.
Existing workflow environments often present configuration challenges in heterogeneous computing and storage infrastructures.
Users face difficulties accessing HPC resources and managing data across distributed systems.

Purpose of the Study:

To introduce Yabi, an open-source software system designed to address complexities in life science workflow execution.
To enable seamless and transparent access to heterogeneous high-performance computing (HPC) environments.
To provide a flexible and secure environment for creating, reusing, and managing analysis workflows and large datasets.

Main Methods:

Described the architecture of the Yabi software system.
Implemented pluggable execution and data backends for adaptability.
Developed both a web-based drag-and-drop interface and a command-line interface for user interaction.
Enabled simplified tool configuration for system administrators via a web interface.

Main Results:

Yabi provides an adaptable analysis workflow environment with pluggable backends.
It enables secure and flexible management of large datasets across geographically distributed compute resources.
The system simplifies tool configuration, reducing overhead for users and administrators.
Demonstrated Yabi's utility through bioinformatics use cases in large-scale biomedical data analysis.

Conclusions:

Yabi abstracts technical HPC complexities, offering an intuitive, scalable, web-based workflow environment.
Users can access tools via drag-and-drop or a command-line interface.
Yabi is deployed at multiple institutions and available for use.