Construction of executable models from text (:py:mod:`biomass.construction`)
============================================================================

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]_.

**References**

.. [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).

.. toctree::
   :maxdepth: 3
   
   thermodynamic_restrictions
   reaction_rules
   text2model
   template