BioJS: an open source JavaScript framework for biological data visualization

Gomez, John; García, Leyla; Salazar, Gustavo; Villaveces, José; Gore, Swanand; García, Alexander; Martı́n, Marı́a Jesús; Launay, Guillaume; Alcántara, Rafael; del-Toro, Noemi; Dumousseau, Marine; Orchard, Sandra; Velankar, Sameer; Hermjakob, Henning; Zong, Chenggong; Ping, Peipei; Corpas, Manuel; Jiménez, Rafael C.

doi:10.1093/bioinformatics/btt100

Cited by 104 publications

(91 citation statements)

References 6 publications

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“…BioJS [6] Framework for biological data visualization, on which several libraries have been built (a collection featuring some of them is available [7]). PhyD3 [8] Library for phylogenetic tree visualization in the browser.…”

Section: Tool and Referencementioning

confidence: 99%

Web Apps Come of Age for Molecular Sciences

Abriata

2017

Informatics

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Whereas server-side programs are essential to maintain databases and run data analysis pipelines and simulations, client-side web-based computing tools are also important as they allow users to access, visualize and analyze the content delivered to their devices on-the-fly and interactively. This article reviews the best-established tools for in-browser plugin-less programming, including JavaScript as used in HTML5 as well as related web technologies. Through examples based on JavaScript libraries, web applets, and even full web apps, either alone or coupled to each other, the article puts on the spotlight the potential of these technologies for carrying out numerical calculations, text processing and mining, retrieval and analysis of data through queries to online databases and web services, effective visualization of data including 3D visualization and even virtual and augmented reality; all of them in the browser at relatively low programming effort, with applications in cheminformatics, structural biology, biophysics, and genomics, among other molecular sciences.

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Section: Tool and Referencementioning

confidence: 99%

Web Apps Come of Age for Molecular Sciences

Abriata

2017

Informatics

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“…[21] It provides a community-driven online repository with a wide range components for visualizing biological data contributed by the bioinformatics community. BioJS builds on node.js 32 providing both server-side and client-side libraries.…”

Section: Visualization Toolsmentioning

confidence: 99%

Building applications for interactive data exploration in systems biology

Fjukstad

Dumeaux

Olsen

et al. 2017

Preprint

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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.

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“…BioJS 6 is an open source JavaScript library of components for visualization of biological data on the web. As a JavaScript component, the HeatMapViewer is very flexible, interactive and webready.…”

Section: Introductionmentioning

confidence: 99%

HeatMapViewer: interactive display of 2D data in biology

et al. 2014

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Summary: The HeatMapViewer is a BioJS component that lays-out and renders two-dimensional (2D) plots or heat maps that are ideally suited to visualize matrix formatted data in biology such as for the display of microarray experiments or the outcome of mutational studies and the study of SNP-like sequence variants. It can be easily integrated into documents and provides a powerful, interactive way to visualize heat maps in web applications. The software uses a scalable graphics technology that adapts the visualization component to any required resolution, a useful feature for a presentation with many different data-points. The component can be applied to present various biological data types. Here, we present two such cases – showing gene expression data and visualizing mutability landscape analysis. Availability: https://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7706.

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BioJS: an open source JavaScript framework for biological data visualization

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 104 publications

References 6 publications

Web Apps Come of Age for Molecular Sciences

Web Apps Come of Age for Molecular Sciences

Building applications for interactive data exploration in systems biology

HeatMapViewer: interactive display of 2D data in biology

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