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Synthea Physiology Simulations

The simulation configuration files in this directory can be used to execute a single run of a Synthea physiology model via the gradle command line interface. The configuration allows manipulation of the differential equation solver, step size, sim duration, and configuration for output charts if desired. Output files will be in the output/physiology directory.

Note that these are only utilized for the physiology gradle command and are not part of the normal Synthea execution procedure.

Usage

./gradlew physiology --args="config/simulations/[config name].yml"

Examples

  ./gradlew physiology --args="config/simulations/circadian_clock.yml"
  ./gradlew physiology --args="config/simulations/ecg.yml"
  ./gradlew physiology --args="config/simulations/insulin_signalling_diabetic.yml"
  ./gradlew physiology --args="config/simulations/insulin_signalling_normal.yml"
  ./gradlew physiology --args="config/simulations/liver_metabolism.yml"
  ./gradlew physiology --args="config/simulations/mammalian_circadian_rhythm_non_24hr.yml"
  ./gradlew physiology --args="config/simulations/menstrual_cycle.yml"
  ./gradlew physiology --args="config/simulations/o2_transport_metabolism.yml"
  ./gradlew physiology --args="config/simulations/plasma_melatonin.yml"  
  ./gradlew physiology --args="config/simulations/pulmonary_fluid_dynamics.yml"
  ./gradlew physiology --args="config/simulations/pulmonary_oxygen_intake.yml"
  ./gradlew physiology --args="config/simulations/telomere_associated_dna_damage.yml"
  ./gradlew physiology --args="config/simulations/weight_change.yml"

Synthea Usage

/run_synthea -s 21 -p 1000 Indiana "Evansville" --physiology.generators.enabled="true" --physiology.state.enabled="true"

Output

Graphs and raw data in CVS files will be found in output/physiology folder.

You may also wish to create a large population of 10,000 or more individuals, and search for gallblader patients (which are currently the only patients that have ECG physiology data attached to them.)

# generate the sample patients
run_synthea -p 10000

# then search for gallbladder conditions with any of the following terms:
  - Media
  - 29303009 
  - Electrocardiogram
  - valueSampledData

References