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The tool simulates an SBML file in [COPASI](http://copasi.org/) and saves the time course data in an [SBtab](https://sbtab.net/) file (*.csv*). The script cannot be run from the terminal, import the script and run the
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method
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#### ```simulate(sbml_file, time_end)```
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* *sbml_file*: filepath of SBML model
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* *time_end*: simulation runtime 0 -> *time_end*
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* *sbml_model*: filepath of SBML model
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* *duration*: simulation runtime 0 -> *time_end*
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## GenerateODEsFromReactions
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**Write ODE dict from reactions dict**
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The script formulates ODEs from reaction information (rate, substrates, products, modifiers, stoichiometries). To work properly it also needs the unit of the species as well as annotations of the species and it's corresponding compartment. The script is called in almost all YCM modules and returns an ODE dictionary. It cannot be called from terminal, import the script and run the method
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#### ```odes = generateODEsFromReactions(reaction_dict, sp_compartment, sp_annotations, units, com_annotations)```
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#### ```odes = generate_odes_from_reactions(reaction_dict, sp_compartment, sp_annotations, units, com_annotations)```
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* *reaction_dict*: dictionary of reactions (*{rate: **str**, substrates: {**str**: **int**}, products: {**str**: **int**}, modifiers: {**str**: **int**}}*
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* *sp_compartment*: dictionary of species localisations
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* *sp_annotations*: dictionary of species annoations
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[**Detailed documentation**](tools_merger)
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## SBML_export
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**SBML export of Python script module file.**
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The tool reads an Python module file (from the */python_modules/* folder) and writes it to an SBML file (to the */SBML_modules/* folder). It can be called directly from terminal:
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## SBML
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**SBML import to and export of Python script module file.**
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The tool reads an Python module file (from the */python_modules/* folder) and writes it to an SBML file (to the */SBML_modules/* folder). It can be called directly from terminal:
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#### ```python SBML_export.py filepath```
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* *filepath*: filepath to module Python script
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## SBML_import
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**SBML import to modeldict instance.**
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Use this tool to read an SBML file and convert it to a modeldict. The modeldict is currently written into a *pickle* file written in the actual working directory. The script can be executed directly from terminal:
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Use this tool to read an SBML file and convert it to a modeldict. The modeldict is currently written into a *pickle* file written in the actual working directory. The script can be executed directly from terminal:
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#### ```python SBML_import.py filepath```
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* *filepath*: filepath to the SBML model
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* *filepath*: filepath of a Python pickle file (*.p*)
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The script can also be called in a Python session:
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#### ```writePythonModule(modeldict, model_name, doc_txt)```
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#### ```write_python_module(modeldict, model_name, doc_txt)```
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* *modeldict*: modeldict of the model
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* *model_name*: name of the model file (default value is the current module name)
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* *doc_txt*: info text for the model (default value is an emtpy string)
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To write a test module with a list of constant species:
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#### ```writePythonTestModule(modeldict, model_name, const_sp)```
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#### ```write_python_tTest_module(modeldict, model_name, const_sp)```
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* *modeldict*: modeldict of the model
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* *model_name*: name of the model file (default value is the current module name)
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* *const_sp*: list of species names to be set constant in the Python file
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