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README.md

[//]: # ( PyPI package ) Documentation Test results Test coverage Code analysis License Analytics

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.

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Generate random whole-cell models

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