How to run
Options (inside [] is default value, allow arbitrary order)
-r FILENAME : output generated reactions to FILENAME -s STEP_NUM : run a simulation with STEP_NUM step [120] -i ITR_NUM : loop reaction genaration with ITR_NUM times [10] -d : allow duplicated rule -t END_TIME : run a simulation by END_TIME(sec)[run a simulation with 120 steps, END_TIME is not defined] -v : print out generated reactions to stdout -l : allow loc[cation] notation (You have to use this option, if you use location info in model.)
When both option "-s" and "-t" are defined, pybngl.py use "-t" option only.
Examples
$ python pybngl.py -s 10 -v test/testToy.py -- run a simulation with the model written in test/testToy.py -- (-s 10) : Number of the ODE step is 10 -- (-v) : print out generated reactions to stdout
$ python pybngl.py -s 0 -i 20 -v test/testLabel.py -- run a simulation with the model written in test/testLabel.py -- (-s 0) : Number of the ODE step is 0 (generate reactions without simulation) -- (-i 20) : loop reaction generation 20 times (it takes long long time...) -- (-v) : print out generated reactions to stdout
$ python pybngl.py -l test/testLoc.py -- run a simulation with the model written in test/testLoc.py -- (-l) : allow loc notation(testLoc.py use loc natation)
test/testConc.py -- a model with user defined function
test/testEgfr.py -- a model with EGF receptor signaling pathway
test/testFunc.py -- a model with user defined function -- definition and usage of functions are written in head of the file
test/testLabel.py -- a model with label(%) notation -- It takes a long time to generate reactions
test/testLoc.py -- a model with loc notation -- needs "-l" option in use
test/testToy.py -- a model with label(%) notation
working/testDuplicatedLabel.py -- a model with optical isomer notatio(_) -- currently not supported