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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

Enis Afgan¹, Clare Sloggett², Nuwan Goonasekera²

¹Victorian Life Sciences Computation Initiative (VLSCI), University of Melbourne, Melbourne, Victoria, Australia; Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America; Centre for Computing and Informatics (CIR), Rudjer Boskovic Institute (RBI), Zagreb, Croatia.

|October 27, 2015

Summary

This summary is machine-generated.

The Genomics Virtual Laboratory (GVL) provides researchers with a flexible, cloud-based platform for complex genomics data analysis. It offers pre-configured tools and scalable resources, simplifying high-throughput data processing and visualization for researchers.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

High-throughput genomics data analysis is complex and resource-intensive.
Researchers face barriers due to the cost and expertise required for computational platforms.
Existing platforms often lack flexibility and scalability for diverse user needs.

Purpose of the Study:

To design and implement a cloud-based platform for genomics analysis.
To provide researchers with accessible, reproducible, and scalable computational resources.
To lower the barrier to entry for high-throughput genomics data analysis.

Main Methods:

Developed the Genomics Virtual Laboratory (GVL) as a middleware layer.
Integrated machine images, cloud management tools, and online services.
Enabled on-demand compute cluster creation with pre-configured bioinformatics tools and datasets.
Supported web-based (Galaxy, RStudio, IPython Notebook) and command-line interfaces.

Main Results:

The GVL offers a flexible platform for building scalable compute clusters.
Users can access a wide range of bioinformatics tools, reference datasets, and visualization options.
The platform supports both web-based and command-line analysis methods.
GVL is available on multiple cloud environments and designed to be cloud-agnostic.

Conclusions:

The Genomics Virtual Laboratory blueprint facilitates cloud-based genomics research.
GVL enhances research capabilities by providing accessible, versatile, and scalable resources.
The platform addresses key logistical and technical constraints in genomics data analysis.