RetroSignalModel
Model schematics:
RetroSignalModel.CONSTANT_SIGNAL
RetroSignalModel.ONE_SIGNAL
RetroSignalModel.RtgMTK
RetroSignalModel.ZERO_SIGNAL
RetroSignalModel.find_steady_states
RetroSignalModel.hil
RetroSignalModel.load_conditions
RetroSignalModel.load_data
RetroSignalModel.load_parameters
RetroSignalModel.optim_params
RetroSignalModel.optim_params_threads
RetroSignalModel.resting_u0
RetroSignalModel.CONSTANT_SIGNAL
— MethodConstant damage signal
RetroSignalModel.ONE_SIGNAL
— FunctionDamage signal = 1
RetroSignalModel.RtgMTK
— FunctionrtgMTK(S = DEFAULT_SIGNAL; name, proteinlevels=STRESSED)
Make a RTG signalling ModelingToolkit (mtk) system with a time-dependent damage signal function S
and proteinlevels
for Rtg1, Rtg2, Rtg3, Bmh, and Mks proteins.
RetroSignalModel.ZERO_SIGNAL
— FunctionDamage signal = 0
RetroSignalModel.find_steady_states
— MethodFind steady states of the ODE system sys
by randomly
RetroSignalModel.hil
— Methodhil(x, k, n=1)
Hill function
\[hil(x, k, n) := rac{x^n}{x^n + k^n}\]
RetroSignalModel.load_conditions
— FunctionLoad boolean conditions for model validation.
RetroSignalModel.load_data
— MethodLoads a CSV file and returns a RowTable (An tuple of NamedTuple for each row)
RetroSignalModel.load_parameters
— FunctionLoad model parameters
RetroSignalModel.optim_params
— FunctionFind parameters that satisfy the boolean conditions in the retrograde (RTG) signalling model using Optimization methods.
RetroSignalModel.optim_params_threads
— FunctionFind n parameter sets using multithreading
RetroSignalModel.resting_u0
— FunctionMake resting initial conditions fot the system. Default to all zeros.