MyBPC
The following test verifies MyBPC kinetics for the 2-state model schematized below.
In this model, MyBPC (yellow) is able to bind to an active actin binding site and transition from an unbound to a bound state.
What this test does
The MyBPC kinetics test:
-
Runs a simulations in which a half-sarcomere is held isometric and activated in a solution with a pCa of 4.5.
-
Saves a status file at each time step, which contains the state of every mybpc molecule.
-
Assesses all the mybpc transitions occuring between two consecutive time-steps, and calculates the apparent rate constants.
-
Compares the calculated rate constants with those provided in the following model file:
"c_kinetics": [
{
"no_of_states": 2,
"max_no_of_transitions": 1,
"scheme": [
{
"number": 1,
"type": "D",
"extension": 0,
"transition": [
{
"new_state": 2,
"rate_type": "gaussian_pc",
"rate_parameters": [
200
]
}
]
},
{
"number": 2,
"type": "A",
"extension": 0.0,
"transition": [
{
"new_state": 1,
"rate_type": "poly",
"rate_parameters": [
150,
1,
2
]
}
]
}
]
}
]
}
Instructions
Before proceeding, make sure that you have followed the installation instructions and that you already tried to run the single trials demos.
Getting ready
-
Open an Anaconda Prompt
- Activate the FiberSim Anaconda Environment by executing:
conda activate fibersim
- Change directory to
<FiberSim_dir>/code/FiberPy/FiberPy
, where<FiberSim_dir>
is the directory where you installed FiberSim.
Run the test
- Type:
python Fiberpy.py run_batch "../../../testing_suite/thick_kinetics/mybpc/batch_c_kinetics.json"
- You should see text appearing in the terminal window, showing that the simulations are running. When it finishes (this can take ~20-30 minutes), you should see something similar to the image below.
Viewing the results
The results and summary figure from the simulation are written to files in <FiberSim_dir>/testing_suite/thick_kinetics/mybpc/sim_output
The hs
folder contains the status files that were dumped at each time-step calculation.
The analysis
folder contains figure files showing the calculated rate laws for all mybpc transitions, as well as the model rate laws.