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Below are lines that can be added to the bottom of BNGL file to customize its SBML output for multicompartment representation. Please note that it works in alpha version only.

Each line starts from #%VC%. This way, BNG engine treats the line as a comment and does not process it. However, the Virtual Cell reads these lines as command lines.

Start BioNetGen@VCell at http://vcell.org/bionetgen

#########################################################################

# Merge reversible reactions - this way, instead of two one-directional reactions the SBML file will have one bidirectional reaction.

#%VC% mergeReversibleReactions

# Use to replace the first pattern (in C syntax) with the second in species names. One can add as many these commands as necessary.

#%VC% speciesRenamePattern("\." , "_")

#%VC% speciesRenamePattern("[\(,][a-zA-Z]\w*", "")

#%VC% speciesRenamePattern("~|!\d*", "")

#%VC% speciesRenamePattern("\(\)", "")

#%VC% speciesRenamePattern("\)", "") setUnit("all", "default") #multiple instructions can appear per line

#%VC% speciesRenamePattern("locN", "Nuc")

#%VC% speciesRenamePattern("locC", "Cyto")

# The first line is used to put species with ~N into Nucleous compartment and place inside Cytosol compartment. # The second line is used to place species with ~C into Cytosol compartment and place it inside environment compartment.

#%VC% compartmentalizeSpecies("loc\([^\)]*?l~N", "Nucleus", "Cytoplasm")

#%VC% compartmentalizeSpecies("loc\([^\)]*?l~C", "Cytoplasm", "environment")

-- MichaelBlinov - 24 Jul 2007

Topic revision: r2 - 2008-01-11 - 16:40:47 - MichaelBlinov
 
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