Table 2

Comparison of non-commercial tools for the network-centered visualization and analysis of biological data
Tasks VANTED CYTOSCAPE ONDEX OMIX CELL PATHVISIO BIOUML VISANT PATHWAY BINA MAPMAN
[[12]] [[54]] [[55]] Designer [[57]] [[58]] [[59]] Projector [[61]] [[62]]
[[56]] [[60]]
Import
 networks + + + + + (+) + (+) + + -
 experimental data + + + + (+) + + - + (+) +
 connection to experiment database + + + - (+) - - - - + -
 connection to network databases + + + - (+) - + + (+) + +
Visualization
 charts on nodes and edges + - - + - - - - + - +
 automatic network layouts + + + + + - + + - + -
 SBGN support + + - - (+) + + - - - -
 flux data support + + - + + - - - (+) + -
 3D visualization + (+) - + - - - - - - -
Integration
 mapping of numerical or + + + + + + - - + + +
 multimodal data
 mapping tables, identifier mapping + + + - - (+) + - + (+) -
 linking other resources + + + + + + + + + - +
Simulation
 constraint-based analysis + (+) - + (+) - - - - - -
 Petri net analysis + - - - (+) - - - - - -
Exploration and interaction
 panning, zooming, collapsing, + + + + (+) (+) + + + + (+)
 search and selection
 network exploration + + + - - (+) + + + + +
 brushing, image exploration + - - - - - - - - - -
Analysis
 networks + + + - (+) - + + - (+) -
 statistics + + + - - + - - - (+) +
 enrichment analysis + + - - - + + + - + +
Export
 raster graphics, vector graphics + + + + + + + + - + (+)
 interactive websites + - - - - (+) + + + - -
 experimental data + + - - + - + - + + -
 networks + + + + + + + (+) - + -

The first column comprises the sub-tasks of Table 1, which are covered by the respective tool. Please note that also add-ons and plugins of the respective system were evaluated. “-” no or inadequate support, “(+)” = partial support, “+” good support of the sub-task.

Rohn et al.

Rohn et al. BMC Systems Biology 2012 6:139   doi:10.1186/1752-0509-6-139

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