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REleased tool that is continuing to actively development new features

cellPACK

cellPack is a specialized implementation of autoPack that packs molecules together with biologically relevant interactions. cellPACK has additional uses for 3D artists.

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Cytoscape

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.   Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization.   Additional features are available as Apps (formerly called Plugins).   Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases.   They may be developed by anyone using the Cytoscape open API based on Java™ technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store.mor

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Institution: UC San Diego

Real-time Neuron Viz

Two novel techniques for view frustum culling based on a bounding volume skeleton which is created from the geometrical skeleton of the neurons. These skeletons are combined with spatial partitions and some GPU processing to extract the portions of the neurons that need to be rendered while still facilitating interactive changes in the attributes. Experimental results show that the proposed method yields better results than classical approaches such as OBB-trees and looks promising for sort-first environments.

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Institution: Universidad Politécnica de Madrid, École Polytechnique Fédérale de Lausanne, Universidad Rey Juan Carlos

This work has been funded by the Spanish Ministry of Education and Science (Cajal Blue Brain project and grant TIN2010-21289-C02-01&02) and the Blue Brain Project.

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