# Smoldyn configuration file to test wildcards in reactions # Units are microns and seconds, numbers are approximately correct for a yeast cell define KTRANSC 0.01 # 100 seconds per transcript define KRIBBIND 0.1 # chosen to give ~1000 proteins define KTRANSL 2 # 2 amino acids per second, should be 20 define KMUT 0.000002 # 0.02 mutations per ((10000 s)*basepair*option) define KRNADEG 0.01 # RNA lifetime of 100 seconds define KPROTDEG 0.01 # protein lifetime of 100 seconds define CELLRAD 2.5 # cell diameter of 5 um define NUCRAD 1 # nuclear diameter of 5 um random_seed 2 # Graphical output graphics opengl graphic_iter 1000 frame_thickness 0 # System space and time definitions dim 3 boundaries x -CELLRAD CELLRAD boundaries y -CELLRAD CELLRAD boundaries z -CELLRAD CELLRAD time_start 0 time_stop 10000 # about 2.5 hours, which is 1-2 cell generations time_step 0.1 # Molecular species and their properties species DnaATCAATATT Rib difc Rib 4 # from eq. in Andrews, 2012 color Rib grey display_size Rib 2 difc Dna* 0.1 # complete guess, assumes DNA is part of chromosome difc_rule Dna* 0.1 difc_rule Rna* 8 difc_rule Prot* 22 # GFP diffusion coefficient color_rule Dna* black color_rule Rna* red color_rule Prot* green color_rule Rna*Rib* lightgreen display_size_rule Dna*|Rna* 4 display_size_rule Prot* 2 display_size_rule Rna*Rib* 4 # Surfaces start_surface cellmembrane color both black polygon both edge action_rule all both reflect panel sphere 0 0 0 CELLRAD 20 20 end_surface start_surface nucmembrane color both purple polygon both edge action_rule Dna*|Rib both reflect action_rule Rna*|Prot* both transmit panel sphere 0 0 0 NUCRAD 10 10 end_surface # Compartments start_compartment nucleus point 0 0 0 surface nucmembrane end_compartment start_compartment cell point 0 0 0 surface cellmembrane end_compartment start_compartment cytoplasm compartment equal cell compartment andnot nucleus end_compartment # Reactions reaction_rule rxnTransc Dna* -> Dna$1 + Rna$1 KTRANSC reaction_rule rxnRibBind Rna*[A,T,C,G] + Rib -> RnaRib*[A,T,C,G]Prot KRIBBIND reaction_rule rxnTranslN Rna*RibAA[T,C]* -> Rna*AA[T,C]Rib*n KTRANSL reaction_rule rxnTranslF Rna*RibTT[T,C]* -> Rna*TT[T,C]Rib*f KTRANSL reaction_rule rxnTranslL Rna*RibTT[A,G]* -> Rna*TT[A,G]Rib*l KTRANSL reaction_rule rxnTranslS Rna*RibTC?* -> Rna*TC?Rib*s KTRANSL reaction_rule rxnTranslY Rna*RibTA[T,C]* -> Rna*TA[T,C]Rib*y KTRANSL reaction_rule rxnTranslW Rna*RibTGG* -> Rna*TGGRib*w KTRANSL reaction_rule rxnTranslL Rna*RibCT?* -> Rna*CT?Rib*l KTRANSL reaction_rule rxnTranslP Rna*RibCC?* -> Rna*CC?Rib*p KTRANSL reaction_rule rxnTranslH Rna*RibCA[T,C]* -> Rna*CA[T,C]Rib*h KTRANSL reaction_rule rxnTranslQ Rna*RibCA[A,G]* -> Rna*CA[A,G]Rib*q KTRANSL reaction_rule rxnTranslR Rna*RibCG?* -> Rna*CG?Rib*r KTRANSL reaction_rule rxnTranslI Rna*RibAT[T,C,A]* -> Rna*AT[T,C,A]Rib*i KTRANSL reaction_rule rxnTranslM Rna*RibATG* -> Rna*ATGRib*m KTRANSL reaction_rule rxnTranslT Rna*RibAC?* -> Rna*AC?Rib*t KTRANSL reaction_rule rxnTranslN Rna*RibAA[T,C]* -> Rna*AA[T,C]Rib*n KTRANSL reaction_rule rxnTranslK Rna*RibAA[G,A]* -> Rna*AA[G,A]Rib*k KTRANSL reaction_rule rxnTranslS Rna*RibAG[T,C]* -> Rna*AG[T,C]Rib*s KTRANSL reaction_rule rxnTranslR Rna*RibAG[G,A]* -> Rna*AG[G,A]Rib*r KTRANSL reaction_rule rxnTranslV Rna*RibGT?* -> Rna*GT?Rib*v KTRANSL reaction_rule rxnTranslA Rna*RibGC?* -> Rna*GC?Rib*a KTRANSL reaction_rule rxnTranslD Rna*RibGA[T,C]* -> Rna*GA[T,C]Rib*d KTRANSL reaction_rule rxnTranslE Rna*RibGA[A,G]* -> Rna*GA[A,G]Rib*e KTRANSL reaction_rule rxnTranslG Rna*RibGG?* -> Rna*GG?Rib*g KTRANSL reaction_rule rxnRibUnbind Rna*RibProt* -> Rna* + Rib + Prot* KTRANSL reaction_rule rxnRnaDeg Rna*[A,T,C,G] -> 0 KRNADEG reaction_rule rxnProtDeg Prot* -> 0 KPROTDEG reaction_rule rxnMut Dna*?* -> Dna*{A|T|C|G}* KMUT reaction_log stdout rxnMut all expand_rules on-the-fly # initial molecules compartment_mol 1 DnaATCAATATT nucleus compartment_mol 100 Rib cytoplasm # a cell really has ~1000 to 10000 output_file expressionout.txt stdout output_format CSV #cmd i 0 10000 10 molcountspecieslist expressionout.txt Rna* Prot* cmd i 0 10000 10 molcountspecieslist expressionout.txt Rna*AAT* Rna* Protini Protiyi cmd A molcountheader stdout cmd A molcount stdout #cmd @ 100 diagnostics all text_display time Dna* Rna* Prot* end_file