Usage

The project is configured to do two main computation:

• Download and simulate BioModels

• Learn the relationship between model’s parameters and moments

Download and Simulate

The fsml.simulate package contains all the utilities to download, transform and simulate a biological model. These biological models are taken directly from the BioModels Database using a Python Package called basico. The goal of this module is to download a biomodel and then simulate it using COPASI multiple times, each with a different model’s parameters configuration. In this way we obtain a number of different simulations, from which it is possible to compute the mean and the variance useful for the next step, i.e., learning.

Here is an example on how to use this package in a script

An example of Download and Simulate

 from fsml.simulate.main import transform_and_simulate_one
 import fsml.utils as utils
 import os.path as opath
 import os

 # Define the output folders
 log_dir = opath.join(os.getcwd(), "log/")
 output_dir = opath.join(os.getcwd(), "runs/")
 data_dir = opath.join(os.getcwd(), "data/")
 test_dir = opath.join(os.getcwd(), "tests/")

 # Define the model ID and the number of simulations
 model_id = 1
 number_of_simulations = 1000

 # Setup the seed
 utils.setup_seed()

 # Run the procedure
 transform_and_simulate_one(prefix_path=test_dir,
                         log_dir=log_dir,
                         output_dir=output_dir,
                         data_dir=data_dir,
                         model_id=model_id,
                         nsim=number_of_simulations,
                         job_id=0,
                         gen_do=False)

In this example, with few lines of code, we are able to simulate the BioModel BIOMD0000000001 (or Edelstein1996 - EPSP ACh event) for a number of 1000 times (each with different parameters). The result of the simulation would be a CSV file stored in the ./data/meanstd folder. The SBML model would be saved into the ./tests/ folder, while all the parameters and the initial values for the species inside the ./log folder. Finally, the ./runs folder is just a temporary directory where the files containing the report produced by COPASI are stored.

Note

If you want also to save all the dense outputs (the trajectory of all the simulations) just set the parameter gen_do of the transform_and_simulate_one function to True.

In this example I have shown how to simply download, transform and simulate one single model. Of course, it can be done with as many models you wants. This is another simple example on how to do that.

Download, transform and simulate 10 models in a row

 # Define how many models
 n_models = 10

 # Define the number of simulations
 number_of_simulations = 1000

 # Setup the seed
 utils.setup_seed()

 for model_id in range(1, n_models + 1):
     # Run the procedure
     transform_and_simulate_one(prefix_path=test_dir,
                             log_dir=log_dir,
                             output_dir=output_dir,
                             data_dir=data_dir,
                             model_id=model_id,
                             nsim=number_of_simulations,
                             job_id=0,
                             gen_do=False)

There is another way to do that (however it is not suggested). In the same package there is a function fsml.simulate.main.transform_and_simulate() which use concurrent processing to simulate multiple models at the same time.

Learning