| Construction of executable models from text (:py:mod:`biomass.construction`) |
| ============================================================================ |
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| The Text2Model class converts texts and sentences on biochemical systems into an executable |
| mathematical model. It was originally developed in the `pasmopy project <https://github.com/pasmopy/pasmopy>`_ [1]_ [2]_. |
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| **References** |
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| .. [1] Imoto, H., Yamashiro, S. & Okada, M. A text-based computational framework for patient |
| -specific modeling for classification of cancers. iScience 25, 103944 (2022). |
| .. [2] Imoto, H., Yamashiro, S., Murakami, K. & Okada, M. Protocol for stratification of |
| triple-negative breast cancer patients using in silico signaling dynamics. |
| STAR Protocols 3, 101619 (2022). |
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| .. toctree:: |
| :maxdepth: 3 |
| |
| thermodynamic_restrictions |
| reaction_rules |
| text2model |
| template |
