Figure 1.

Model representations. (a) Typical cartoon diagrams and schematic interactions (adapted from [28]). Shapes, styles and colors are arbitrary. (b) The zoomed-in part of the cartoon diagram in (a) translated into a logic model. Shapes and arrow styles are represented in Systems Biology Graphical Notation (SBGN) standard (Entity Relationship (ER) format) that provide a defined one-to-one correspondence with a logic formalism. Arrows correspond to activation reactions. (c) A truth table corresponding to the logic model in (b) that shows how presence (1) or absence (0) of molecules of the input nodes leads to presence or absence of activity in the selected molecules of interest (output nodes). (d) Dynamic representation of the same model in SBGN standard (Process Diagram (PD) format). It can be considered either as a logic model or as a reaction diagram for a kinetic time-course simulation, where every node represents concentration of a chemical species.

Blinov and Moraru BMC Biology 2012 10:92   doi:10.1186/1741-7007-10-92
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