Here is an ever growing collection of links related to the BrainFrame project.
Information and Knowledge Visualization
Infovis.info section on graph visualization. Lots of great example applications here.
InfoVis:Wiki. The community platform for the information and knowledge visualization community.
knowledge-visualization.org. A good source for foundational information about knowledge visualization.
Gapminder.org. A nice example of visualizing a large data set using animation and graphs.
Nodes3D. A really nice looking 3D graph visualization of connectivity in the brain that is used to interact with data obtained from brainmaps.org.
Brain Visualization
Brainmaps.org. "BrainMaps.org is an interactive multiresolution next-generation brain atlas that is based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet."
Neuron PRM. A tool to visualize and autogenerate mouse cortical neural networks.
Neuroinformatics
Bibliography of Neuroinformatics. A large, well-kept, and frequently updated bibliography of neuroinformatics references, databases, and efforts.
Jena
Jess and other Potential Rule Engines
Jess: Rete Engine. Jess is free to use for research but not free for commercial use. If you want to distribute an application that uses Jess, you need to apply for a separate license.
FuzzyJ ToolKit & FuzzyJess. A Java toolkit that can be used with Jess for the handling of fuzzy concepts and reasoning.
REWERSE Rule Markup Language project.
Pellet. An OWL DL strict open source reasoner. Basic information about using Pellet with Jena can be found here. The Javadocs for Pellet have virtually no comments!
Bossam Rule/OWL Reasoner. No information there on interoperability with Jena, but the documentation for Bossam seems alot better than Pellet.
XML and XML-based Formats
SVG Wiki. A wiki for the SVG user community.
Java
Phys2D Library. And the Javadocs for that library.
Batik: Java SVG Toolkit. A fair;y complete library for the SVG file format.
Processing Libraries
AI Libraries for Processing Some fairly limited AI libraries for processing: Genetic Algorithms and an A* Pathfinder.
Cell Noise Algorithm Libraries
Library for Tablet Integration.
Library for Reading and Writing XML files. This builds upon the core library in Processing for XML.
unleckker lib. A bunch of utility libraries that includes some classes for solving complex polygon intersection tests :)
Ontology Development Links
Managing Ontology Imports. A tutorial about how to manage imports of external ontologies within your own ontology.
MultiAgent Architectures
Semantic Web
SemWebCentral. A repository of tools for the semantic web.
Other (as yet unclassified) Links
Tree of Life Web Project. "The Tree of Life Web Project (ToL) is a collaborative effort of biologists from around the world. On more than 9000 World Wide Web pages, the project provides information about the diversity of organisms on Earth, their evolutionary history (phylogeny), and characteristics."
Numenta Platform for Intelligent Computing. New research grade computing platform that claims to be modeled on the human cortex (which translates to: modeled on how someone thinks the cortex works--not that that is a bad thing).
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