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In both examples, a VRML 3D model file was created containing only the single desired chemical structure.
The IGS absolute antenna model file was used and ocean loading coefficients were obtained from Scherneck (2013) for each of the sites processed.
GC model file was used to adjust the signal intensity values for CNV calling.
The modified gene model file was added to the bitbucket repository subdirectory titled BlastxAnalysis/results as V_corymbosum_scaffold_May_2013_wDescr.bed.gz.gz
The sheep GC model file was generated by calculating the GC content of the 1 Mb genomic region surrounding each marker (500 Kb each side).
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Finally, to facilitate the retrieval of modeling results, all *.pdf files created based on a given model file are stored into a single subfolder named according to the model file name.
For this example, the resulting model file is given as Additional file 14.
This model file is then loaded into Virtools, and via this existing prototyping program, lights and exploration controls are added.
The canonical model file is provided as an.xml file and can be viewed using CellDesigner.
The GDI-integrated model file is provided as an.xml file and can be viewed using CellDesigner.
Finally, the model file is made available, together with its documentation in the Supplementary material 2to this article.
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