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This article describes a computational framework for cell biological modeling and simulation that is based on the mapping of experimental biochemical and electrophysiological data onto experimental images.
Tools exist like the Pathway Tools Omics-Viewer [47] which allow the mapping of experimental data of identified metabolites onto pathways.
The integrated pathway map of Pathway Projector is based on the widely used layout of the KEGG Atlas with the addition of nodes for genes and enzymes for the mapping of experimental data from transcriptomic, proteomic, and metabolomic experiments.
Practically, any reconstruction algorithm requires mapping of experimental images onto the surface of a scattering object.
Modules to support import of different pathway exchange formats (BioPax), visual mapping of experimental data on pathway components in Payao, would be developed in future versions.
Integrating VistaClara directly into Cytoscape enables several useful coordinated interactions: Mapping of experimental conditions is easily managed by simply clicking on the appropriate table column header to select that column for network node coloring.
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Figure 4 Map of experimental sites (processed after [27]).
Figure 6 Map of experimental sites (processed after Banat Map) [40].
Table 1 Map of experimental groups into cooling groups for analysis Animal group Volume cooling (VC) No volume cooling (NVC) No cooling (NC) Femoral saline n = 3 X Femoral slurry n = 3 X Carotid saline n = 5 X Carotid slurry n = 3 X Alsius IVTM n = 3 X RhinoChill n = 3 X Ice bags n = 3 X Control n = 3 X.
Since pathways are essentially connected in vivo, the use of a global map is desirable, especially for the mapping of comprehensive experimental data.
The mapping of numerical experimental data such as concentrations and ratios is done through a color encoding and rectangles in the SVG image representing genes, proteins or metabolites are subdivided.
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