JavaScript Libraries for Informatics

During our monthly San Diego Informatics Lunch meeting, the topic of conversation was JavaScript libraries for informatics.  Over the past few years the term “thick client application” has gradually morphed from a reference to desktop applications, to JavaScript-heavy browser-based applications.  Driven in part by libraries like jQuery, Angular.js, Backbone.js, and Ember, these frameworks (along with the adoption of HTML5) have enabled applications that weren’t previously possible in a browser.

Kei Ono, lead developer from UCSD’s Cytoscape project, remarked that at a recent meeting on visualization, there were no projects with desktop applications.

In preparation for the meeting, I did a brief survey of JavaScript libraries with the following results:

BioJS – Built by the folks at EBI, BioJS provides a series of components for visualizing sequence and structure information.  Here’s a video from last year’s GMOD meeting that describes the project.

ChemWriter – built by MetaMolecular, this pure JavaScript library makes it possible to edit 2D chemical structures.

Cytoscape.js – The Cytoscape.js framework provides a means for visualizing networked biological data in a browser.  With the latest release of the Cytoscape Java application you can now export network data in JSON format, and visualize it in a web page using the Cytoscape.js library.

jBio – referring to itself as “BioPerl in JavaScript”, jBio is a jQuery-based library for manipulating and visualizing sequence data.

JBrowse – This library makes it easy to create your own genome browser.

jsMol – Is a transpiled version of jMol that allows users to view 3D molecular structures without having Java installed.

jsMolEdit – a library for editing and viewing 2D chemical structures. The library makes use of GWT.

jsPhylosvg – is a library for rendering phylogenetic trees.

OneZoom – another library for rendering phylogenetic trees.

Scribl – is a JavaScript library for visualizing “genomic regions, alignments and assembly data”.

SMS – The rather unfortunately named, Sequence Manipulation Suite, is a library for manipulating sequence data.

By-and-large, the JavaScript components were dedicated to visualizing data in the browser.  If anyone has a library that they’d like to add to the list, leave a comment below.


About Mark Fortner

I write software for scientists doing drug discovery and cancer research. I'm interested in Design Thinking, Agile Software Development, Web Components, Java, Javascript, Groovy, Grails, MongoDB, Firebase, microservices, the Semantic Web Drug Discovery and Cancer Biology.
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