biocrnpyler.mechanisms.txtl

Classes

Energy_Transcription_MM(rnap, fuels[, ...])

Michaelis Menten Transcription that consumed energy.

Energy_Translation_MM(ribosome, fuels[, ...])

Michaelis Menten Translation that consumes energy species.

NegativeHillTranscription([name, mechanism_type])

A mechanism to model transcription as a proprotional negative hill function: G --> G + P rate = k*G*(1)/(K+R^n) where R is a regulator (repressor).

OneStepGeneExpression([name, mechanism_type])

A mechanism to model gene expression without transcription or translation.

PositiveHillTranscription([name, mechanism_type])

A mechanism to model transcription as a proprotional positive hill function: G --> G + P rate = k*G*(R^n)/(K+R^n) where R is a regulator (activator).

SimpleTranscription([name, mechanism_type])

A Mechanism to model simple catalytic transcription.

SimpleTranslation([name, mechanism_type])

A mechanism to model simple catalytic translation.

Transcription_MM(rnap[, name])

Michaelis Menten Transcription.

Translation_MM(ribosome[, name])

Michaelis Menten Translation.

multi_tl(ribosome[, name, mechanism_type])

Multi-RBZ Translation w/ Isomerization.

multi_tx(pol[, name, mechanism_type])

Multi-RNAp Transcription w/ Isomerization.
class biocrnpyler.mechanisms.txtl.Energy_Transcription_MM(rnap: Species, fuels: List[Species], wastes=typing.List[biocrnpyler.core.species.Species], name='energy_transcription_mm', **keywords)[source]

Michaelis Menten Transcription that consumed energy.

G + RNAP <–> G:RNAP Fuel + G:RNAP –> G + RNAP + T + Fuel (Transcription can only happen when there is fuel)

at rate ktx/L (length dependent transcription rate)

Fuel + G:RNAP –> G:RNAP +wastes (Fuel consumption treated faster)

at rate ktx (This occurs L times faster than the above, resulting in the correct fuel use)

Initializes a Transcription_MM instance. :param fuels: List of Species consumed during transcription :param wastes: List of Species consumed during transcription :param rnap: Species instance that is representing an RNA polymerase :param name: name of the Mechanism, default: transcription_mm

update_reactions(dna, component, part_id=None, complex=None, transcript=None, protein=None, **keywords)[source]

the child class should implement this method.

Returns:

empty list

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

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.txtl.Energy_Translation_MM(ribosome: Species, fuels: List[Species], wastes=typing.List[biocrnpyler.core.species.Species], name='energy_translation_mm', **keywords)[source]

Michaelis Menten Translation that consumes energy species.

mRNA + Rib <–> mRNA:Rib (binding) fuels + mRNA:Rib –> mRNA + Rib + Protein + fuels (translation) fuels + mRNA:Rib –> mRNA:Rib +wastes (fuel consumption)

Initializes a Translation_MM instance.

Parameters:

  • ribosome – Species instance that is representing a ribosome

  • fuels – List of fuel Species that are consumed during translation

  • wastes – List of Species consumed during translation

  • name – name of the Mechanism, default: energy_translation_mm

update_reactions(transcript, protein, component, part_id=None, complex=None, **keywords)[source]

the child class should implement this method.

Returns:

empty list

update_species(transcript, protein, **keywords)[source]

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.txtl.NegativeHillTranscription(name='negativehill_transcription', mechanism_type='transcription')[source]

A mechanism to model transcription as a proprotional negative hill function: G –> G + P rate = k*G*(1)/(K+R^n) where R is a regulator (repressor). Optionally includes a leak reaction G –> G + P @ rate kleak.

Initializes a NegativeHillTranscription instance.

Parameters:

  • name – name of the Mechanism, default: negativehill_transcription

  • mechanism_type – type of the Mechanism, default: transcription

update_reactions(dna, regulator, component, part_id, transcript=None, leak=False, protein=None, **keywords)[source]

This always requires the inputs component and part_id to find the relevant parameters

Parameters:

  • dna

  • regulator

  • component

  • part_id

  • transcript

  • leak

  • protein

  • keywords

Returns:

update_species(dna, regulator, transcript=None, leak=False, protein=None, **keywords)[source]

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.txtl.OneStepGeneExpression(name='gene_expression', mechanism_type='transcription')[source]

A mechanism to model gene expression without transcription or translation.

G –> G + P

Initializes a OneStepGeneExpression instance.

Parameters:

  • name – name of the Mechanism, default: gene_expression

  • mechanism_type – type of the Mechanism, default: transcription

update_reactions(dna, component=None, kexpress=None, protein=None, transcript=None, part_id=None, **keywords)[source]

the child class should implement this method.

Returns:

empty list

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

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.txtl.PositiveHillTranscription(name='positivehill_transcription', mechanism_type='transcription')[source]

A mechanism to model transcription as a proprotional positive hill function: G –> G + P rate = k*G*(R^n)/(K+R^n) where R is a regulator (activator). Optionally includes a leak reaction G –> G + P @ rate kleak.

Initializes a PositiveHillTranscription instance.

Parameters:

  • name – name of the Mechanism, default: positivehill_transcription

  • mechanism_type – type of the Mechanism, default: transcription

update_reactions(dna, regulator, component, part_id, transcript=None, leak=False, protein=None, **keywords)[source]

This always requires the inputs component and part_id to find the relevant parameters

Parameters:

  • dna

  • regulator

  • component

  • part_id

  • transcript

  • leak

  • protein

  • keywords

Returns:

update_species(dna, regulator, transcript=None, leak=False, protein=None, **keywords)[source]

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.txtl.SimpleTranscription(name='simple_transcription', mechanism_type='transcription')[source]

A Mechanism to model simple catalytic transcription.

G –> G + T

Initializes a SimpleTranscription instance.

Parameters:

  • name – name of the Mechanism, default: simple_transcription

  • mechanism_type – type of the Mechanism, default: transcription

update_reactions(dna, component=None, ktx=None, part_id=None, transcript=None, protein=None, **keywords)[source]

the child class should implement this method.

Returns:

empty list

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

the child class should implement this method.

Returns:

empty list

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

A mechanism to model simple catalytic translation.

T –> T + P

Initializes a SimpleTranslation instance.

Parameters:

  • name – name of the Mechanism, default: simple_translation

  • mechanism_type – type of the Mechanism, default: translation

update_reactions(transcript, component=None, ktl=None, part_id=None, protein=None, **keywords)[source]

the child class should implement this method.

Returns:

empty list

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

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.txtl.Transcription_MM(rnap: Species, name='transcription_mm', **keywords)[source]

Michaelis Menten Transcription.

G + RNAP <–> G:RNAP –> G+RNAP+mRNA

Initializes a Transcription_MM instance.

Parameters:

  • rnap – Species instance that is representing an RNA polymerase

  • name – name of the Mechanism, default: transcription_mm

update_reactions(dna, component, part_id=None, complex=None, transcript=None, protein=None, **keywords)[source]

the child class should implement this method.

Returns:

empty list

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

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.txtl.Translation_MM(ribosome: Species, name='translation_mm', **keywords)[source]

Michaelis Menten Translation.

mRNA + Rib <–> mRNA:Rib –> mRNA + Rib + Protein

Initializes a Translation_MM instance.

Parameters:

  • ribosome – Species instance that is representing a ribosome

  • name – name of the Mechanism, default: translation_mm

update_reactions(transcript, protein, component, part_id=None, complex=None, **keywords)[source]

the child class should implement this method.

Returns:

empty list

update_species(transcript, protein, **keywords)[source]

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.txtl.multi_tl(ribosome: Species, name: str = 'multi_tl', mechanism_type: str = 'translation', **keywords)[source]

Multi-RBZ Translation w/ Isomerization.

Detailed translation mechanism accounting for each individual RBZ occupancy states of mRNA. Still needs some work, so use with caution, read all warnings and consult the example notebook.

n ={0, max_occ} mRNA:RBZ_n + RBZ <–> mRNA:RBZ_n_c –> mRNA:RBZ_n+1 mRNA:RBZ_n –> mRNA:RBZ_0 + n RBZ + n Protein mRNA:RBZ_n_c –> mRNA:RBZ_0_c + n RBZ + n Protein

n –> number of open configuration RBZ on mRNA max_occ –> Physical maximum number of RBZ on mRNA (based on RBZ and mRNA dimensions) mRNA:RBZ_n –> mRNA with n open configuration RBZ on it mRNA:RBZ_n_c –> mRNA with n open configuration RBZ and 1 closed configuration RBZ on it

For more details, see examples/MultiTX_Demo.ipynb

Initializes a multi_tl instance.

Parameters:

  • ribosome – a Species instance that represents a ribosome

  • name – name of the Mechanism, default: multi_tl

  • mechanism_type – type of the Mechanism, default: translation

update_reactions(transcript, protein, component, part_id, **keywords)[source]

It sets up the following reactions.

mRNA:RBZ_n + RBZ <–> mRNA:RBZ_n_c –> mRNA:RBZ_n+1 kf1 = kbr, kr1 = kur, kf2 = k_iso_r mRNA:RBZ_n –> mRNA:RBZ_0 + n RBZ + n Protein kf = ktl_solo mRNA:RBZ_n_c –> mRNA:RBZ_0_c + n RBZ + n Protein kf = ktl_solo

update_species(transcript, protein, component, part_id, **keywords)[source]

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.txtl.multi_tx(pol: Species, name: str = 'multi_tx', mechanism_type: str = 'transcription', **keywords)[source]

Multi-RNAp Transcription w/ Isomerization.

Detailed transcription mechanism accounting for each individual RNAp occupancy states of gene.

n ={0, max_occ} DNA:RNAp_n + RNAp <–> DNA:RNAp_n_c –> DNA:RNAp_n+1 DNA:RNAp_n –> DNA:RNAp_0 + n RNAp + n mRNA DNA:RNAp_n_c –> DNA:RNAp_0_c + n RNAp + n mRNA

n –> number of open configuration RNAp on DNA max_occ –> Physical maximum number of RNAp on DNA (based on RNAp and DNA dimensions) DNA:RNAp_n –> DNA with n open configuration RNAp on it DNA:RNAp_n_c –> DNA with n open configuration RNAp and 1 closed configuration RNAp on it

For more details, see examples/MultiTX_Demo.ipynb

Initializes a multi_tx instance.

Parameters:

  • pol – reference to a species instance that represents a polymerase

  • name – name of the Mechanism, default: multi_tx

  • mechanism_type – type of the mechanism, default: transcription

  • keywords

update_reactions(dna, transcript, component, part_id, protein=None, **keywords)[source]

It sets up the following reactions.

DNA:RNAp_n + RNAp <–> DNA:RNAp_n_c –> DNA:RNAp_n+1 kf1 = k1, kr1 = k2, kf2 = k_iso DNA:RNAp_n –> DNA:RNAp_0 + n RNAp + n mRNA kf = ktx_solo DNA:RNAp_n_c –> DNA:RNAp_0_c + n RNAp + n mRNA kf = ktx_solo

max_occ = maximum occupancy of gene (physical limit)

update_species(dna, transcript, component, part_id, protein=None, **keywords)[source]

the child class should implement this method.

Returns:

empty list