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.
- Install dependencies
- 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
Please see the API documentation.
The build utilities are released under the MIT license.
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.