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Table 9 Programming languages and libraries to build visual prototype

From: Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

Language/Library

Description

URL

Adobe Edge

Animated, interactive web content for projects that previously required Flash

https://creative.adobe.com/products/animate

Arbor.js

Efficient, force-directed layout algorithm plus abstractions for graph organization and screen refresh handling

http://arborjs.org/

Biojs

BioJS enables a full-featured biological workbench directly in your browser

http://biojs.net/

Bonsai.js

Lightweight graphics library with an intuitive graphics API and an SVG renderer

https://bonsaijs.org/

Chart.js

Object oriented client side graphs. Data visualization in six animated, fully customizable chart types

http://www.chartjs.org/

Cube

Time-series data, built on MongoDB, Node and D3. Real-time visualizations of aggregate metrics

https://square.github.io/cube/

Cubism

D3 plugin for visualizing time series

https://square.github.io/cubism/

Cytoscape Web

Easily embed interactive networks in your website

http://cytoscapeweb.cytoscape.org/

D4

Friendly charting domain-specific language for D3

https://github.com/heavysixer/d4

Easeljs

API to work with rich graphics and interactivity with HTML5 Canvas

http://www.createjs.com/EaselJS

Ember Charts

Ember.js and d3.js based time series, bar, pie and scatter charts that are easy to extend and modify

http://addepar.github.io/

Envision

Fast, dynamic and interactive HTML5 visualizations

http://www.humblesoftware.com/envision

Flare

Interactive data visualizations in Flash (ActionScript)

http://flare.prefuse.org/

Foamtree

Tree map visualization with innovative layout algorithms and animations such as Voronoi Treemaps

http://carrotsearch.com/foamtree-overview

Highcharts.js

HTML5/JavaScript-based line, spline, area, area-spline, column, bar, pie, scatter, angular gauges, area-range, area-spline-range, column-range, bubble, box plot, error bars, funnel, waterfall and polar charts

http://www.highcharts.com/

Infovis Toolkit

A comprehensive range of tools for creating Interactive Data Visualizations for the Web

http://philogb.github.io/jit/

Jgrapht

A free Java graph library that provides mathematical graph-theory objects and algorithms

http://jgrapht.org/

Kartograph

Kartograph is a simple and lightweight framework for creating beautiful, interactive vector maps

http://kartograph.org/

Matplotlib

A Python 2D plotting library that produces publication quality figures

http://matplotlib.org/

Miso

Interactive storytelling and data visualization content

http://misoproject.com/

Netadvantage

Charts with a range of frameworks including asp.net and Silverlight. Visualization options include bar, bubble, Gantt, line, radial, scatter, spline and doughnut charts

http://www.infragistics.com/products

Orange

Data mining through visual programming or Python scripting. Components for machine learning. Add-ons for bioinformatics and text mining. Packed with features for data analytics

http://orange.biolab.si/

Paper.js

A vector graphics scripting framework that runs on top of the HTML5 Canvas

http://paperjs.org/

Pivotviewer

A Silverlight control that makes it easier to interact with massive amounts of data on the web

http://www.microsoft.com/silverlight/pivotviewer/

Polychart.js

A JavaScript graphing library capable of producing a wide array of graphics fairly easily

http://www.polychartjs.com/

Prefuse

Java-based interactive data. Data structures for tables, graphs and trees, a host of layout and visual encoding techniques, animation, dynamic queries, integrated search and database connectivity

http://prefuse.org/

Prefuse Flare

Visualization and animation for ActionScript. From basic charts and graphs to complex interactive graphics. Data management, visual encoding, animation and interaction techniques

http://flare.prefuse.org/

Ractive.js

It transforms templates into blueprints for apps that are interactive by default. Two-way binding, animations, SVG support and more

http://www.ractivejs.org/

Raphael.js

JavaScript library for vector graphics on the web. To create a specific chart or image. Crop and rotate widget

http://raphaeljs.com/

Rcharts

R package to create, customize and publish interactive JavaScript visualizations from R using a familiar lattice style plotting interface

http://rcharts.io/

Seaborn

A Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics

http://stanford.edu/~mwaskom/software/seaborn/

Shiny

A web application framework for R to turn an analysis into interactive web applications. No HTML, CSS or JavaScript knowledge required

http://shiny.rstudio.com/

Sigma.js

A JavaScript library dedicated to graph drawing. It makes easy to publish networks on Web pages and allows developers to integrate network exploration in rich web applications

http://sigmajs.org/

Three.js

A lightweight cross-browser JavaScript library/API used to create and display animated 3D computer graphics on a web browser that supports WebGL

http://threejs.org/

Timeline.js

Visually rich interactive timelines, available in 40 languages

http://timeline.knightlab.com/

Variance

Build powerful data visualizations for the web without writing JavaScript. Wide range of visualizations

https://variancecharts.com/

Vega

A visualization grammar, a declarative format for creating, saving and sharing visualization designs. Data visualizations in JSON format and interactive views using either HTML5 Canvas or SVG

http://trifacta.github.io/vega/

Vida.io

A way to build reusable cloud visualizations: clone visualization templates, customize without coding skills and embed or share in the cloud

https://vida.io/

Vis

A data visualization platform designed to assist investigative journalists, activists and others in mapping complex business or crime networks

http://vis.occrp.org/

Visual Sedimentation

A JavaScript library for visualizing streaming data, inspired by the process of physical sedimentation. jQuery (to facilitate HTML and JavaScript development) and Box2DWeb (for physical world simulation)

http://www.visualsedimentation.org/

WebGL

A JavaScript API for rendering interactive 3D computer graphics and 2D graphics within any compatible web browser without the use of plugins

https://www.khronos.org/webgl/