1. COLOUR SCHEME 1b GREEN varX Auxiliary Units Logical gates Entity Pool Nodes and operator LABEL pre:label unspecified entity unit of information ? // or operator value state variable LABEL simple chemical not operator LABEL LABEL macromolecule Process nodes marker clone markers LABEL association LABEL genetic entity dissociation Complex process N:2 LABEL uncertain process multimer INFO omitted process N:2 N:2 LABEL LABEL LABEL LABEL Arcs N:2 LABEL LABEL production source/sink catalysis LABEL Submap Compartment tag stimulation LABEL inhibition observable INFO Necessary stimulation LABEL LABEL perturbation modulation

2. varX COLOUR SCHEME 1a GREEN Auxiliary Units Entity Pool Nodes Logical gates LABEL unspecified entity pre:label unit of information and operator // ? value state variable or operator LABEL simple chemical not operator LABEL LABEL macromolecule marker Process nodes clone marker LABEL LABEL genetic entity association dissociation Complex process N:2 LABEL multimer INFO uncertain process N:2 omitted process N:2 LABEL LABEL LABEL LABEL N:2 LABEL LABEL Arcs source/sink production Submap LABEL catalysis Compartment tag stimulation LABEL INFO observable inhibition LABEL Necessary stimulation perturbation LABEL modulation

3. varX COLOUR SCHEME 2b BLUE Auxiliary Units Entity Pool Nodes Logical gates LABEL unspecified entity and operator pre:label unit of information // ? or operator value state variable LABEL simple chemical LABEL not operator clone markers marker LABEL macromolecule Process nodes LABEL association genetic entity dissociation Complex process N:2 LABEL INFO multimer uncertain process omitted process N:2 LABEL LABEL N:2 LABEL LABEL N:2 LABEL LABEL Arcs source/sink production LABEL catalysis Submap Compartment tag stimulation LABEL INFO observable inhibition LABEL Necessary stimulation LABEL perturbation modulation

4. varX COLOUR SCHEME 2a BLUE Auxiliary Units Entity Pool Nodes Logical gates LABEL unspecified entity pre:label unit of information and operator ? // value state variable or operator LABEL simple chemical not operator LABEL LABEL macromolecule marker Process nodes clone marker LABEL LABEL genetic entity association dissociation Complex process N:2 LABEL multimer INFO uncertain process N:2 omitted process N:2 LABEL LABEL LABEL LABEL N:2 LABEL LABEL Arcs source/sink production LABEL Submap catalysis tag Compartment stimulation LABEL observable INFO inhibition LABEL Necessary stimulation perturbation LABEL modulation