timecourse¶
The timecourse of a roadrunner model which is simulated in parts.
A model of a tissue (the tissue and perfusion models of pkdb_models, a
zonated liver) is often simulated in parts: a part sets values of the model at
its start (a perfusion, a substrate, a switch) and runs for its duration, the
next part continues from the state in which the part before ends. A
Simulation is the list of its parts, run_simulation runs them one after the
other and returns one timecourse whose time continues over the parts.
The parts run on a roadrunner instance of the model directly, without the experiments of sbmlsim: the model is loaded, its tolerances and its selections are set by the script which runs it.
dataclass
¶
A part of a simulation.
Attributes:
| Name | Type | Description |
|---|---|---|
tend |
float
|
the duration of the part, in the time unit of the model. |
changes |
dict[str, float]
|
the values the part sets at its start, by the selection of
roadrunner ( |
steps |
int
|
the number of steps of the timecourse of the part; the
timecourse has |
dataclass
¶
A simulation of parts which run one after the other.
Attributes:
| Name | Type | Description |
|---|---|---|
sid |
str
|
the id of the simulation, e.g. the key of its results. |
title |
str
|
the title of the simulation, e.g. of its figures. |
parts |
list[SimPart]
|
the parts, in the order in which they run. |
Run the parts of a simulation and concatenate their timecourses.
The model is reset (resetAll) before the first part, so that a
simulation does not depend on the simulations before it. A part sets its
changes and simulates from the state in which the part before ends; the
time of its timecourse continues the time of the part before, so the last
point of a part and the first point of the next part have the same time
(the state before and after the changes). The columns are the
timeCourseSelections of r.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
r
|
RoadRunner
|
the roadrunner instance of the model. |
required |
sim
|
Simulation
|
the simulation. |
required |
Returns:
| Type | Description |
|---|---|
DataFrame
|
The timecourse of the simulation, the timecourses of its parts one |
DataFrame
|
after the other (the index of each part starts at 0). |