Batch

Overview

Batch structures are stored in JSON format. MATMyoSim uses batch structures to run sets of simulations. An example would be generating a tension-pCa curve. Each simulation in the batch is a job.

More details

Each job must define files describing

a protocol
a model
simulation options
an output file

Caveat on figures

MATMyoSim uses a parfor loop to run jobs in parallel. As a result, it won’t display figures defined in the options structure.

If you want to check individual jobs (which is nearly always a good idea), run them individually as opposed to using a batch strcture.

Example

{
    "MyoSim_batch":
    {
        "job":
        [
            {
                "protocol_file_string": "sim_input/90/protocol_90.txt",
                "model_file_string": "sim_input/model_file.json",
                "options_file_string": "sim_input/sim_options.json",
                "results_file_string": "../../temp/sim_output/90/results_90.myo"
            },
            {
                "protocol_file_string": "sim_input/58/protocol_58.txt",
                "model_file_string": "sim_input/model_file.json",
                "options_file_string": "sim_input/sim_options.json",
                "results_file_string": "../../temp/sim_output/58/results_62.myo"
            },
            {
                "protocol_file_string": "sim_input/45/protocol_45.txt",
                "model_file_string": "sim_input/model_file.json",
                "options_file_string": "sim_input/sim_options.json",                
                "results_file_string": "../../temp/sim_output/45/results_45.myo"
            }
        ]
    }
}