Figure 3.

Iterative model building and validation as a tool to guide and validate network reconstruction. (A) Idealised workflow for model building: Model extensions and improvements are done in small steps, with each step being evaluated as a Boolean model. (B) The rxncon database underlying the Boolean model is fully compatible with the other rxncon features, including a range of visualisations and automatic model generation in formats suitable for quantitative modelling. (C) The iterative improvement applied on the yeast MAP kinase network. Only a limited number of changes were needed to make the HOG, PKC and MAT pathways functional (Figure 5), most of which are in line with existing knowledge as discussed in the main text. The single largest change was the addition of 50 hypothetical dephosphorylation reactions (Additional file 3: Table S3).