Figure 5

The network reconstruction workflow. The first phase of the process was the network reconstruction itself, where we extracted reaction and contingency information from published data. The curation process produced the initial network reconstruction (NR1). The second phase of the process was the validation and iterative improvement. It starts with the creation of the bBM, followed by simulation of the bBM and comparison to the known input/output relationships. If the model fails to transmit information as expected, the gap is identified and filled, and the updated network re-enters the workflow at model creation. If the model passes all tests, it is accepted and considered a validated network (NR2). The validated network constitutes a knowledge resource, but can also be further processed with the rxncon tool to generate graphical or mathematical models in a range of formats, as illustrated by the rule-based model (Supplementary file 4).