3.1.1.1.1.1. etfl.analysis.dynamic

ME-related Reaction subclasses and methods definition

3.1.1.1.1.1.1. Module Contents

3.1.1.1.1.1.1.1. Classes

EnzymeDeltaRHS

E(t+dt) - E(t) <= f(dt, E(t), mu)

mRNADeltaRHS

F(t+dt) - F(t) <= f(dt, F(t), mu)

3.1.1.1.1.1.1.2. Functions

add_enzyme_ref_variable(dmodel)

add_mRNA_ref_variable(dmodel)

add_enzyme_rhs_variable(dmodel)

add_mRNA_rhs_variable(dmodel)

get_mu_times_var(dmodel, macromolecule)

add_enzyme_delta_constraint(dmodel, timestep, degradation, synthesis)

Adds the constraint

add_mRNA_delta_constraint(dmodel, timestep, degradation, synthesis)

Adds the constraint

add_dynamic_variables_constraints(dmodel, timestep, dynamic_constraints)

apply_ref_state(dmodel, solution, timestep, has_mrna, has_enzymes, mode='backward')

param dmodel

update_sol(t, X, S, dmodel, obs_values, colname)

update_medium(t, Xi, Si, dmodel, medium_fun, timestep)

compute_center(dmodel, objective, provided_solution=None, revert_changes=True)

Fixes growth to be above computed lower bound, finds chebyshev center,

show_initial_solution(model, solution)

run_dynamic_etfl(model, timestep, tfinal, uptake_fun, medium_fun, uptake_enz, S0, X0, step_fun=None, inplace=False, initial_solution=None, chebyshev_bigm=BIGM, chebyshev_variables=None, chebyshev_exclude=None, chebyshev_include=None, dynamic_constraints=DEFAULT_DYNAMIC_CONS, mode='backward')

param model

the model to simulate

wrap_time_sol(var_solutions, obs_values)

3.1.1.1.1.1.1.3. Attributes

mrna_length_avg

DEFAULT_DYNAMIC_CONS

BIGM

ETFL.mrna_length_avg = 370
ETFL.DEFAULT_DYNAMIC_CONS
class ETFL.EnzymeDeltaRHS

Bases: etfl.optim.variables.EnzymeVariable

E(t+dt) - E(t) <= f(dt, E(t), mu) E(t+dt) <= E(t) + f(dt, E(t), mu) E(t+dt) <= ERHS(t, E(t), mu)

prefix = ERHS_
class ETFL.mRNADeltaRHS

Bases: etfl.optim.variables.mRNAVariable

F(t+dt) - F(t) <= f(dt, F(t), mu) F(t+dt) <= F(t) + f(dt, F(t), mu) F(t+dt) <= FRHS(t, F(t), mu)

prefix = FRHS_
ETFL.add_enzyme_ref_variable(dmodel)
ETFL.add_mRNA_ref_variable(dmodel)
ETFL.add_enzyme_rhs_variable(dmodel)
ETFL.add_mRNA_rhs_variable(dmodel)
ETFL.get_mu_times_var(dmodel, macromolecule)
ETFL.add_enzyme_delta_constraint(dmodel, timestep, degradation, synthesis)

Adds the constraint

E-Eref <= Δt*v_assembly_max E-Eref-Δt*v_assembly_max <= 0

Parameters

  • dmodel –

  • timestep –

Returns

ETFL.add_mRNA_delta_constraint(dmodel, timestep, degradation, synthesis)

Adds the constraint

Parameters

  • dmodel –

  • timestep –

Returns

ETFL.add_dynamic_variables_constraints(dmodel, timestep, dynamic_constraints)
ETFL.apply_ref_state(dmodel, solution, timestep, has_mrna, has_enzymes, mode='backward')
Parameters

  • dmodel –

  • solution –

  • timestep –

  • has_mrna –

  • has_enzymes –

  • mode – `forward’ or `backward’ for the integration scheme

Returns

ETFL.update_sol(t, X, S, dmodel, obs_values, colname)
ETFL.update_medium(t, Xi, Si, dmodel, medium_fun, timestep)
ETFL.compute_center(dmodel, objective, provided_solution=None, revert_changes=True)

Fixes growth to be above computed lower bound, finds chebyshev center, resets the model, returns solution data

Parameters

  • dmodel –

  • objective – the radius to maximize

Returns

ETFL.show_initial_solution(model, solution)
ETFL.BIGM = 1000
ETFL.run_dynamic_etfl(model, timestep, tfinal, uptake_fun, medium_fun, uptake_enz, S0, X0, step_fun=None, inplace=False, initial_solution=None, chebyshev_bigm=BIGM, chebyshev_variables=None, chebyshev_exclude=None, chebyshev_include=None, dynamic_constraints=DEFAULT_DYNAMIC_CONS, mode='backward')
Parameters

  • model – the model to simulate

  • timestep – the time between each step of the integration

  • tfinal – The stopping time

  • uptake_fun – Functions that regulate the uptakes (Michaelis Menten etc.)

  • medium_fun – Functions that regulates the medium concentrations (switches, bubbling diffusion, etc…)

  • uptake_enz – If specified, will use the enzyme kcats for the uptake functions

  • S0 – Initial concentrations

  • X0 – Initial amount of cells

  • step_fun – Function for additional operations on the model at each time step (extra kinetics, etc …)

  • inplace –

  • initial_solution – Used for setting growth rate lower bound

  • chebyshev_bigm –

  • chebyshev_variables –

  • chebyshev_exclude –

  • chebyshev_include –

  • dynamic_constraints –

  • mode – `forward’ or `backward’ for the Euler integration scheme

Returns

ETFL.wrap_time_sol(var_solutions, obs_values)