Cytoscape is an open source software platform for visualizing data networks and pathways. Though designed for bioinformatic systems, it has been generalized to complex network analysis and has applications extending to the semantic web. Its core distribution has basic features for data integration and visualization, with additional features available via Java-based plugins.

The JavaScript InfoVis Toolkit is a free set of tools for creating interactive data visualizations compatible with web standards. Visualization options include bar graphs, radial graphs, tree graphs and more, many integrating animations.

Graphviz is a free, open source graph visualization tool in constant development since 1988. It represents structural information as diagrams of abstract graphs and networks.

Project Quincy is a free, open source Django application and MySQL database for tracing the development of social networks and instititions across time and space. Aimed at historians, it enables users to map networks in historical documentation such as biographic, organizational, correspondance or location. Creator Jean Bauer has developed Project Quincy as a single generalizable and extensible database with applications beyond mapping historic connections. All code is available via Github repository, or by contacting the creator directly.

Omeka is a content management system designed for the display of library, museum, archives, and scholarly collections and exhibitions.

Omeka falls at a crossroads of Web Content Management, Collections Management, and Archival Digital Collections Systems. Omeka is designed with non-IT specialists in mind, allowing users to focus on content and interpretation rather than programming. It brings Web 2.0 technologies and approaches to academic and cultural websites to foster user interaction and participation. It makes top-shelf design easy with a simple and flexible templating system. Its robust open-source developer and user communities underwrite Omeka’s stability and sustainability.

Omeka allows users to publish cultural heritage objects, extend its functionality with themes and plugins, and curate online exhibits with digital objects.

Modest Maps is a small Javascript library for interactive tile-based maps that can display maps from external sources (e.g. OpenStreetMap, but not commercial layers like Google Maps), enable panning and zooming, and track the position of points based on XML data. It is designed to be lightweight and offer a minimal set of features, and therefore has less functionality than Leaflet, a similar tool.

960 Grid System is a CSS template that comes with corresponding Acorn, Fireworks, Flash, InDesign, GIMP, Inkscape, Illustrator, OmniGraffle, Photoshop, QuarkXPress, Visio, Exp Design, and printable templates to facilitate different stages of the web design process.

The HTML5 boilerplate is a set of HTML/CSS/JS templates for building websites. It offers cross-browser compatibility, caching and compression rules, mobile browser optimizations, graceful degradation, and IE-specific classes.