Construction of executable models from text (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 [1] [2].
References
- Thermodynamic restrictions (
biomass.construction.thermodynamic_restrictions) - Available reaction rules (
biomass.construction.reaction_rules)ReactionRulesReactionRules.input_txtReactionRules.similarity_thresholdReactionRules.parametersReactionRules.speciesReactionRules.reactionsReactionRules.differential_equationsReactionRules.obs_descReactionRules.param_infoReactionRules.init_infoReactionRules.param_constraintsReactionRules.param_excludedReactionRules.fixed_speciesReactionRules.sim_tspanReactionRules.sim_conditionsReactionRules.sim_unperturbedReactionRules.rule_wordsReactionRules.nothingReactionRules.fwd_arrowsReactionRules.double_arrowsReactionRules._bind_and_dissociate()ReactionRules.dimerize()ReactionRules.bind()ReactionRules.is_phosphorylated()ReactionRules.is_dephosphorylated()ReactionRules.phosphorylate()ReactionRules.dephosphorylate()ReactionRules.transcribe()ReactionRules.synthesize()ReactionRules.is_synthesized()ReactionRules.degrade()ReactionRules.is_degraded()ReactionRules.translocate()ReactionRules.state_transition()ReactionRules.user_defined()
- Text-to-model conversion (
biomass.construction.text2model) - Template for BioMASS model construction (
biomass.construction.template)