ChiBE is implemented in Java and built on top of ChiEd 2.0, a generic graph visualization tool based on the Eclipse Graph Editing Framework 3.1.1.
The generic biological network visualization tool Cytoscape (Shannon et al., 2003) provides an excellent environment to implement combined analysis and visualization methods.
Expression data were analyzed using Epclust, a generic data clustering, visualization and analysis tool [ 21].
SpotXplore is a plugin for the widely adopted generic Cytoscape network visualization software.
Until lately, it was not very well supported by visualisation and editing tools, but a graphical displayer for SMARTS was recently released [41], and various structure editors provide support for SMARTS editing, including the PubChem chemical structure editor [42], although without yet making use of the SMARTS Viewer visualization for generic features.
Probe set and deleted genome block information were coded using the General Feature Format GFFF version 2, or GFF2) and loaded directly into the genome visualization tool, Generic Genome Browser (GBROWSE) [ 35], which was preloaded with gene model annotation data.
In addition, array data and genome annotation are displayed using a Generic Genome Browser, available for visualization at http://epigara.biologie.ens.fr/index.html.html
While it can provide a geometric zooming visualization of a generic SBML model (e.g., a signaling network), the knowledge-based generalization, and therefore semantic zooming, depends on the ChEBI ontology and is intended for metabolic models.
The COAST project at CEA/IRFU at Saclay, started in 2005, involves astrophysicists and software engineers developing simulation codes in magneto-hydrodynamics and generic tools for data structuration and visualization.
