biocrnpyler.mechanisms.SimpleTranslation

class biocrnpyler.mechanisms.SimpleTranslation(name='simple_translation', mechanism_type='translation')[source]

Bases: Mechanism

Simple catalytic translation mechanism.

A ‘translation’ mechanism that models translation as a single catalytic reaction where mRNA directly produces protein without explicitly modeling ribosome binding and unbinding. This simplified mechanism is appropriate when ribosome dynamics are fast compared to other processes.

The reaction follows the schema:

\[{\text{T}} \rightarrow {\text{T}} + {\text{P}} \]

where T is the transcript (mRNA) and P is the protein.

Parameters:

  • name (str, default 'simple_translation') – Name identifier for this mechanism instance.

  • mechanism_type (str, default 'translation') – Type classification of this mechanism.

Attributes:

  • name (str) – Name of the mechanism instance.

  • mechanism_type (str) – Type classification (‘translation’).

See also

Translation_MM

Explicit Michaelis-Menten translation.

SimpleTranscription

Simple transcription mechanism.

Mechanism

Base class for all mechanisms.

Notes

This mechanism is appropriate for modeling scenarios where:

  • Ribosome dynamics are fast and at quasi-steady-state

  • The focus is on protein-level regulation

  • Computational efficiency is prioritized

The catalytic abstraction treats the mRNA as a template that is not consumed in the reaction. The mRNA persists and can produce multiple protein copies.

Common applications include:

  • Basic translation models

  • Models where ribosomes are not limiting

  • Constitutive protein expression

Required parameters for this mechanism:

  • ‘ktl’ : Translation rate constant

Examples

Model simple translation:

>>> gene = bcp.DNAassembly(
...     name='dna_assembly',
...     promoter='pconst', rbs='RBS_medium', protein='GFP')
>>> tl_mechanism = bcp.SimpleTranslation()
>>> mixture = bcp.Mixture(
...     components=[gene],
...     mechanisms={
...         'transcription': bcp.SimpleTranscription(),
...         'translation': tl_mechanism
...     },
...     parameter_file='mixtures/pure_parameters.tsv'
... )
>>> mixture.compile_crn()

Methods

update_reactions

Generate reactions for simple translation.

update_species

Generate species for simple translation.
update_reactions(transcript, component=None, ktl=None, part_id=None, protein=None, **kwargs)[source]

Generate reactions for simple translation.

Creates a single mass-action reaction representing translation from mRNA to protein.

Parameters:

  • transcript (Species) – The mRNA transcript species that produces protein.

  • component (Component, optional) – Component containing parameter values. Required if ktl is not provided directly.

  • ktl (Parameter or float, optional) – Translation rate constant. If None, retrieved from component parameters.

  • part_id (str, optional) – Identifier for parameter lookup in the component’s parameter database.

  • protein (Species, optional) – The protein species produced.

  • **kwargs – Additional keyword arguments (unused).

Returns:

List containing a single mass-action reaction for translation if transcript is not None, otherwise empty list.

Return type:

list of Reaction

Raises:

ValueError – If component is None and ktl is not provided.

Notes

The reaction has the form:

\[{\text{mRNA}} \rightarrow {\text{mRNA}} + {\text{Protein}} \quad ({\text{rate}} = {\text{ktl}}) \]

The mRNA is catalytic and appears on both sides of the reaction. If transcript is None (only occurs in mixtures without transcription), no reactions are generated.

update_species(transcript, protein=None, **kwargs)[source]

Generate species for simple translation.

Returns the transcript and protein species involved in the translation reaction. If protein is None, creates a default protein species based on the transcript name.

Parameters:

  • transcript (Species) – The mRNA transcript species that produces protein.

  • protein (Species or list of Species, optional) – The protein species produced. If None, a default protein with the same name as the transcript is created. Can be a single Species or a list.

  • **kwargs – Additional keyword arguments (unused).

Returns:

List containing [transcript] plus protein species (single or list).

Return type:

list of Species