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rand_wc_model_gen

The whole-cell model generator generates synthetic whole-cell model descriptions that are used to test downstream components of the whole-cell (WC) modeling pipeline. In particular, these synthetic models can be used to test model description systems and model simulators.

To test modeling pipeline components, synthetic WC models are better than WC models of real cells for several reasons:

• Synthetic models are scalable
• Synthetic models can have unusual properties
• Synthetic models can be generated quickly

This initial version of the model generator creates reaction network models.

Installation

1. Install dependencies
2. Install this package

   pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils
   pip install git+https://github.com/KarrLab/obj_tables.git#egg=obj_tables
   pip install git+https://github.com/KarrLab/wc_kb.git#egg=wc_kb
   pip install git+https://github.com/KarrLab/wc_lang.git#egg=wc_lang
   pip install git+https://github.com/KarrLab/wc_analysis.git#egg=wc_analysis
   pip install git+https://github.com/KarrLab/wc_kb_gen.git#egg=wc_kb_gen
   pip install git+https://github.com/KarrLab/wc_model_gen.git#egg=wc_model_gen
   pip install git+https://github.com/KarrLab/wc_sim.git#egg=wc_sim
   pip install git+https://github.com/KarrLab/wc_test.git#egg=wc_test
   pip install git+https://github.com/KarrLab/rand_wc_model_gen.git#egg=rand_wc_model_gen
   

Documentation

Please see the API documentation.

License

The build utilities are released under the MIT license.

Development team

This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York, USA.

Questions and comments

Please contact the Karr Lab with any questions or comments.