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ComModelPy is a collection of Python [dataclasses](https://docs.python.org/3/library/dataclasses.html) and associated functions which aim to help one in generating stoichiometric metabolic models of communities which consist of one or multiple species. All dataclasses and functions are based on [cobrapy](https://github.com/opencobra/cobrapy).
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CommModelPy is a collection of Python [dataclasses](https://docs.python.org/3/library/dataclasses.html) and associated functions which aim to help one in generating stoichiometric metabolic models of communities which consist of one or multiple species. All dataclasses and functions are based on [cobrapy](https://github.com/opencobra/cobrapy).
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The underlying methods for the generation and analysis of the community models is explained in more detail in ComModelPy's source code documentation.
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The underlying methods for the generation and analysis of the community models is explained in more detail in CommModelPy's source code documentation.
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An exemplary usage of ComModelPy is given in its publiation (Bekiaris & Klamt, in submission).
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An exemplary usage of CommModelPy is given in its publiation (Bekiaris & Klamt, in submission).
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## Installation procedure
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### Option 1: As PyPI module
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You can install ComModelPy as Python module from [PyPI](https://pypi.org/project/commodelpy/) using *pip*:
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You can install CommModelPy as Python module from [PyPI](https://pypi.org/project/commmodelpy/) using *pip*:
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<pre>
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pip install commodelpy
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pip install commmodelpy
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</pre>
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Afterwards, you can use ComModelPy just as any other Python module using *import* in your Python session/script:
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Afterwards, you can use CommModelPy just as any other Python module using *import* in your Python session/script:
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<pre>
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import commodelpy
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import commmodelpy
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</pre>
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In order to import ComModelPy's main script with all major dataclasses and functions and which is called "commodelpy.py", you can import it using
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In order to import CommModelPy's main script with all major dataclasses and functions and which is called "commmodelpy.py", you can import it using
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<pre>
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import commodelpy.commodelpy
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import commmodelpy.commmodelpy
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</pre>
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### Option 2: Direct download
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If you don't want to use ComModelPy as PyPI module, you can also download this repository directly. The main script file is the commodelpy.py Python script in the "commodelpy" subfolder.
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If you don't want to use CommModelPy as PyPI module, you can also download this repository directly. The main script file is the commmodelpy.py Python script in the "commmodelpy" subfolder.
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## Repository structure
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* The actual commodelpy pip package can be found in the "commodelpy" subfolder, where "commodelpy.py" contains all relevant functions and dataclasses.
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* All Python scripts which were used in ComModelPy's publication, which use ComModelPy's function for community models without defined growth and with fixed species ratios, can be found in the "publication_runs" subfolder, which is in the "commodelpy" subfolder. The scripts in the local subfolder "toy_model" contain the script for the generation of the toy model shown in the publication. The scripts in the local subfolder "ecoli_models" contain the generation of dG0 data using the [Equilibrator API](https://gitlab.com/equilibrator/equilibrator-api) as well as the ComModelPy-assisted generation of iML1515 and EcoliCore2 single-species community models. A complete call of all E. coli model scripts in the right order is given by the "execute_publication_ecoli_model_scripts.py" script in the main folder, a call of the toy model scripts is given by the "execute_publication_toy_model_script.py" script in the main folder.
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* An exemplary usage of ComModelPy with its function with a defined fixed growth rate and free species ratios can be found in the "balanced_growth_example" subfolder. A call of the relevant script is given in the "execute_balanced_growth_example.py" script in the main folder.
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* The actual commmodelpy pip package can be found in the "commmodelpy" subfolder, where "commmodelpy.py" contains all relevant functions and dataclasses.
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* All Python scripts which were used in CommModelPy's publication, which use CommModelPy's function for community models without defined growth and with fixed species ratios, can be found in the "publication_runs" subfolder, which is in the "commmodelpy" subfolder. The scripts in the local subfolder "toy_model" contain the script for the generation of the toy model shown in the publication. The scripts in the local subfolder "ecoli_models" contain the generation of dG0 data using the [Equilibrator API](https://gitlab.com/equilibrator/equilibrator-api) as well as the CommModelPy-assisted generation of iML1515 and EcoliCore2 single-species community models. A complete call of all E. coli model scripts in the right order is given by the "execute_publication_ecoli_model_scripts.py" script in the main folder, a call of the toy model scripts is given by the "execute_publication_toy_model_script.py" script in the main folder.
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* An exemplary usage of CommModelPy with its function with a defined fixed growth rate and free species ratios can be found in the "balanced_growth_example" subfolder. A call of the relevant script is given in the "execute_balanced_growth_example.py" script in the main folder.
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## Documentation
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A documentation of ComModelPy's features and functions can be found in the "docs/commodelpy/" subfolder of this repository. The documentation's starting point is "index.html". The whole documentation was generated using [pdoc3](https://github.com/pdoc3/).
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A documentation of CommModelPy's features and functions can be found in the "docs/commmodelpy/" subfolder of this repository. The documentation's starting point is "index.html". The whole documentation was generated using [pdoc3](https://github.com/pdoc3/).
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You can also access ComModelPy's documentation using Python's help function after importing ComModelPy, e.g. for the whole module:
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You can also access CommModelPy's documentation using Python's help function after importing CommModelPy, e.g. for the whole module:
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<pre>
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help(commodelpy)
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help(commmodelpy)
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</pre>
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## Publication
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ComModelPy is published in the following publication:
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CommModelPy is published in the following publication:
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* Bekiaris & Klamt, 2021, *in submission*
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## License
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ComModelPy is free and open source, using the Apache License, Version 2
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CommModelPy is free and open source, using the Apache License, Version 2
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