Rules Railroad - visualizing rule-based models

Visualization conventions

• We demonstrate comparison between bnglViz that illustrates rule-based modeling as a set of individual cartoons describing interactions, and Rules Railroad that illustrates rule-based modeling as a connected network of molecules that is controlled by the rules
• Compartments are ignored and not visualized in RRR, but are accounted for in bnglViz
• Reaction rates and some features like functions are ignored and not visualized in both RRR and bnglViz
• Advantage: color-agnostic: while colors are added for visual enhancement (e.g., green corresponds to forming a bond, red to breaking), the diagrams can still be read without them (by using symbols, e.g., arrows and their directions)

BNGL code	Rules Railroad visualization	bnglViz visualization
begin molecules EGFR(l,r,Y1068~u~p,Y1148~u~p)
begin species EGFR(l,r,Y1068~u,Y1148~u) EGFR(l,r,Y1068~P!1,Y1148~P).Grb2(SH2!1,SH3)
begin observables EGFR(l,r,Y1068~u,Y1148~u~p) EGFR(l,r!+,Y1068~u)
begin reaction rules non-reversible binding rules EGFR(Y1068~p)+Grb2(SH2,SH3) -> EGFR(Y1068~p!1).Grb2(SH2!1,SH3) EGFR(Y1068~p!1).Grb2(SH2!1,SH3) -> EGFR(Y1068~p)+Grb2(SH2,SH3)
reversible binding rules EGFR(Y1068~p)+Grb2(SH2,SH3) <-> EGFR(Y1068~p!1).Grb2(SH2!1,SH3) EGFR(Y1068~p!1).Grb2(SH2!1,SH3) <-> EGFR(Y1068~p)+Grb2(SH2,SH3) EGFR(Y1068~p).Grb2(SH2,SH3!+) <-> EGFR(Y1068~p!1).Grb2(SH2!1,SH3!+)
state transition rules EGFR(Y1068~p)+PTP() -> EGFR(Y1068~u)+PTP() EGFR(r!+,Y1068~u).Src() -> EGFR(r!+,Y1068~p).Src() EGFR(r!+,Y1068~u) -> EGFR(r!+,Y1068~p)
synthesis, degradation rules pro_EGF() -> EGF() EGF().EGFR() -> EGFR() EGF(r!1).EGFR(l!1,r) -> EGFR(l,r)