begin compartments
Cyt 3 1
EC 3 1
M 2 1 NB: The first number after the compartment name is the dimension, and the next is the size. So, M is 2D membrane while Cyt and EC are volumetric cytosil and extracellular space. These definitions are not compatible with cBNGL but used by VCell software only.
begin molecules
1 EGFR(ecd,tmd,Y1~u~p,Y2~u~p) #EGF receptorNB: 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.
This block can be omitted, and BioNetGen will find molecules by processing species and reaction rules.
begin species
1 egfr(l,r,Y1068~Y,Y1148~Y) egfr_tot #unphosphorylated receptorNB: 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.
This block can NOT be omitted.
begin reaction rules
1 egfr(l,r,Y1068~Y,Y1148~Y) egfr_tot #unphosphorylated receptorNB: 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.
This block can NOT be omitted. For details of notations (?, | under site shape, grey vs color, etc)
refer to Faeder et al., 2009.
