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Building applications for interactive data exploration in systems biology

Bjørn Fjukstad, View ORCID ProfileVanessa Dumeaux, View ORCID ProfileKarina Standahl Olsen, View ORCID ProfileMichael Hallet, View ORCID ProfileEiliv Lund, View ORCID ProfileLars Ailo Bongo
doi: https://doi.org/10.1101/141630
Bjørn Fjukstad
1Department of Computer Science, UiT The Arctic University of Norway
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Vanessa Dumeaux
2Department of Biology, Concordia University
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Karina Standahl Olsen
3Department of Community Medicine, UiT The Arctic University of Norway
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Michael Hallet
2Department of Biology, Concordia University
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Eiliv Lund
3Department of Community Medicine, UiT The Arctic University of Norway
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Lars Ailo Bongo
1Department of Computer Science, UiT The Arctic University of Norway
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Abstract

As the systems biology community generates and collects data at an unprecedented rate, there is a growing need for interactive data exploration tools to explore the datasets. These tools need to combine advanced statistical analyses, relevant knowledge from biological databases, and interactive visualizations in an application with clear user interfaces. To answer specific research questions tools must provide specialized user interfaces and visualizations. While these are application-specific, the underlying components of a data analysis tool can be shared and reused later. Application developers can therefore compose applications of reusable services rather than implementing a single monolithic application from the ground up for each project.

Our approach for developing data exploration applications in systems biology builds on the microservice architecture. Microservice architectures separates an application into smaller components that communicate using language-agnostic protocols. We show that this design is suitable in bioinformatics applications where applications often use different tools, written in different languages, by different research groups. Packaging each service in a software container enables re-use and sharing of key components between applications, reducing development, deployment, and maintenance time.

We demonstrate the viability of our approach through a web application, MIxT blood-tumor, for exploring and comparing transcriptional profiles from blood and tumor samples in breast cancer patients. The application integrates advanced statistical software, up-to-date information from biological databases, and modern data visualization libraries.

The web application for exploring transcriptional profiles, MIxT, is online at mixt-blood-tumor.bci.mcgill.ca and open-sourced at github.com/fjukstad/mixt. Packages to build the supporting microservices are open-sourced as a part of Kvik at github.com/fjukstad/kvik.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 24, 2017.
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Building applications for interactive data exploration in systems biology
Bjørn Fjukstad, Vanessa Dumeaux, Karina Standahl Olsen, Michael Hallet, Eiliv Lund, Lars Ailo Bongo
bioRxiv 141630; doi: https://doi.org/10.1101/141630
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Building applications for interactive data exploration in systems biology
Bjørn Fjukstad, Vanessa Dumeaux, Karina Standahl Olsen, Michael Hallet, Eiliv Lund, Lars Ailo Bongo
bioRxiv 141630; doi: https://doi.org/10.1101/141630

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