Rules_Rail_Road - 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_Rail_Road 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 convenience (green corresponds to forming a bond, and it is like green light that opens the traffic alo ....
• OPEN ISSUES: + vs . - possible red/green box???
• OPEN ISSUES: SYNTHESIS, DEGRADATION, CHANGE OF MOLECULE = COMBINATION OF SYNTHESIS AND DEGRADATION ???

BNGL code	Rules_Rail_Road visualization	bnglViz visualization
begin molecules 1 EGFR(ecd,tmd,Y1~u~p,Y2~u~p) #EGF receptor NB: The first number is optional and not included in BNGL processing or visualization. Instead of begin molecules the block may start with begin molecular types.
begin species 1 egfr(l,r,Y1068~Y,Y1148~Y) egfr_tot #unphosphorylated receptor NB: The first number is optional and not included in BNGL processing or visualization. Instead of begin species the block may start with begin seed species.
begin reaction rules 1 egfr(l,r,Y1068~Y,Y1148~Y) egfr_tot #unphosphorylated receptor NB: The symbols before : is reaction rule order - it is optional and not included in BNGL processing or visualization. Instead of begin reaction rules the block may start with begin rules or begin reactions. For details of notations (?, | under site shape, grey vs color, etc) refer to Faeder et al., 2009.