The BioJS article collection of open source components for biological data visualisation

Corpas, Manuel

doi:10.12688/f1000research.3-56.v1

Cited by 5 publications

(4 citation statements)

References 18 publications

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“…, 2013 ), InnateDB ( Breuer K et al. , 2013 ), BioJS library components ( Corpas M, 2014 ), the Saccharomyces genome database (Costanzo MC et al. , 2013), the RCyjs Bioconductor package ( http://www.bioconductor.org/packages/ release/bioc/html/RCyjs.html), the upcoming release of GeneMANIA ( Warde-Farley et al.…”

Section: Featuresmentioning

confidence: 99%

Cytoscape.js: a graph theory library for visualisation and analysis

et al. 2015

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Summary: Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js.Availability and implementation: Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org.Contact: gary.bader@utoronto.ca

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Section: Featuresmentioning

confidence: 99%

Cytoscape.js: a graph theory library for visualisation and analysis

et al. 2015

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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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“…There are solutions in other languages: a Java and JavaScript tool 1 , 2 that can be used for protein visualization. For visualization on the internet, there is also the BioJS solution, which can be used for proteins 3 . Both of these tools are useful but not easily integrated into the Bioconductor workflow.…”

Section: Introductionmentioning

confidence: 99%

drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics

Brennan

2018

F1000Res

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Protein schematics are valuable for research, teaching and knowledge communication. However, the tools used to automate the process are challenging. The purpose of the drawProteins package is to enable the generation of schematics of proteins in an automated fashion that can integrate with the Bioconductor/R suite of tools for bioinformatics and statistical analysis. Using UniProt accession numbers, the package uses the UniProt API to get the features of the protein from the UniProt database. The features are assembled into a data frame and visualized using adaptations of the ggplot2 package. Visualizations can be customised in many ways including adding additional protein features information from other data frames, altering colors and protein names and adding extra layers using other ggplot2 functions. This can be completed within a script that makes the workflow reproducible and sharable.

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The BioJS article collection of open source components for biological data visualisation

Cited by 5 publications

References 18 publications

Cytoscape.js: a graph theory library for visualisation and analysis

Cytoscape.js: a graph theory library for visualisation and analysis

Web Apps Come of Age for Molecular Sciences

drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics

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