BNGL import erroneously scales initial conditions by 2e-5

[CodeByDrescher]

When BNGL is imported and option "Molecules" is selected, all initial counts are multiplied by 2e-5. No scaling (everything is OK) when "Concentration" option is selected.

[vcellmike]

Save this file with .bngl extension and import with volume 1: once as Concentrations (no changes), once with Molecules - all initial counts will be scaled.

begin model
begin parameters
kp1 1.667e-06 # ligand-monomer binding, units: /molecule/s
km1 0.06 # ligand-monomer dissociation, units: /s
end parameters
begin molecule types
egf(r)
egfr(l,r,Y1068YpY)
end molecule types
begin seed species
egf(r) 1.2e6
egfr(l,r,Y1068~Y) 1.8e5
end seed species
begin reaction rules
egfr(l,r) + egf(r) <-> egfr(l!1,r).egf(r!1) kp1, km1 #ligand-monomer
end reaction rules
begin observables
Molecules Efgr_total egfr()
end observables
end model

[danv61]

Clarification from Michael: if "molecules" are selected during import, the number specified in the bngl input file is to be considered as the absolute number of molecules, regardless of volume.
For example, egfr(l,r,Y1068~Y) 1.8e5 means we have 1.8e5 molecules in our volume.

[ACowan0105]

Jim thinks it is ignoring the volume = 1 (or uses that as an extra scalar for default cell volume) and instead using 1/50,000 as a scale factor because default cell size is 50,000 cubic microns.