Screenshot of the Visual Editor of a toy model in ProMoT (left) and of its visually processed export (right), (e.g. to CellNetAnalyzer). The text in the bottom of the right figure shows an incomplete textual export (where '!' denotes Not, '·' represents AND, and '→' activation. Note how, in the Visual Editor, inhibition is encoded by a not element between the compound and the gate and, after applying the visual scenario, it is represented by a single red-colored connection line (but could be easily changed to another color value). Additionally, the direction is indicated by an arrow symbol (different for activation and inhibition), which is implicitly defined in the mathematical description. Furthermore, the element k3r has been hidden, since it belongs to the class reservoir and has thus no biological meaning. Complete textual exports, as well as alternative visualizations, can be found in Tables 1-2 and Figure 4, respectively.
Saez-Rodriguez et al. BMC Bioinformatics 2006 7:506 doi:10.1186/1471-2105-7-506