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Cytoscape project needs your support! Please cite either of the following papers when you use Cytoscape in your publications, which is very important to sustain our federal funding. Melissa S Cline, Michael Smoot, Ethan Cerami, Allan Kuchinsky, Nerius Landys, Chris Workman, Rowan Christmas, Iliana Avila-Campilo, Michael Creech, Benjamin Gross, Kristina Hanspers, Ruth Isserlin, Ryan Kelley, Sarah Killcoyne, Samad Lotia, Steven Maere, John Morris, Keiichiro Ono, Vuk Pavlovic, Alexander R Pico, Aditya Vailaya, Peng-Liang Wang, Annette Adler, Bruce R Conklin, Leroy Hood, Martin Kuiper, Chris Sander, Ilya Schmulevich, Benno Schwikowski, Guy J Warner, Trey Ideker & Gary D Bader

Cytoscape: An Open Source Platform for Complex-Network Analysis and Visualization

http://www.cytoscape.org/

Gephi, an open source graph visualization and manipulation software

Gephi is an interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs. Latest News https://gephi.org/

Processing.org

http://processing.org/ Processing is an open source programming language and environment for people who want to create images, animations, and interactions. Initially developed to serve as a software sketchbook and to teach fundamentals of computer programming within a visual context, Processing also has evolved into a tool for generating finished professional work. Today, there are tens of thousands of students, artists, designers, researchers, and hobbyists who use Processing for learning, prototyping, and production. To contribute to the development, please visit Processing on Google Code to read instructions for downloading the code , building from the source , reporting and tracking bugs , and creating libraries and tools .
Over the last year or so, I’ve spent almost as much time thinking about how to teach data visualization as I’ve spent working with data. I’ve been a teacher for 10 years – for better or for worse this means that as I learn new techniques and concepts, I’m usually thinking about pedagogy at the same time. Lately, I’ve also become convinced that this massive ‘open data’ movement that we are currently in the midst of is sorely lacking in educational components. The amount of available data, I think, is quickly outpacing our ability to use it in useful and novel ways. How can basic data visualization techniques be taught in an easy, engaging manner? This post, then, is a first sketch of what a lesson plan for teaching Processing and data visualization might look like. http://blog.blprnt.com/blog/blprnt/your-random-numbers-getting-started-with-processing-and-data-visualization

Your Random Numbers – Getting Started with Processing and Data Visualization | blprnt.blg

http://mbostock.github.com/protovis/ex/

Protovis - Examples

The final release of Protovis was v3.3.1 (4.7 MB) . The Protovis team is now developing a new visualization library, D3.js , with improved support for animation and interaction. D3 builds on many of the concepts in Protovis; for more details, please read the introduction and browse the examples .