https://github.com/ecell/reaction_reader

https://github.com/ecell/reaction_reader

Last synced: about 2 months ago
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• Host: GitHub
• URL: https://github.com/ecell/reaction_reader
• Owner: ecell
• Created: 2011-06-07T09:49:49.000Z (over 13 years ago)
• Default Branch: master
• Last Pushed: 2012-10-10T06:58:35.000Z (about 12 years ago)
• Last Synced: 2024-03-26T07:44:16.896Z (9 months ago)
• Language: Python
• Homepage:
• Size: 773 KB
• Stars: 1
• Watchers: 8
• Forks: 0
• Open Issues: 17
• Metadata Files:
  • Readme: README

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README

        
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How to use pybngl.py

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How to run

  - $ python pybngl.py [options] [simfile]

    -- options : options, see below.

    -- simfile : simulation model file name.

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)

-------------------

Model samples

-------------------

  - 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