Physiology Models - Rebase

[awatson1978]

Rebuild of PR #1254

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.

Configuration

You will need to set the following two fields to true in the src/main/resources/synthea.properties file.

# Use physiology simulations to generate some VitalSigns
physiology.generators.enabled = true

# Allow physiology module states to be executed
# If false, all Physiology state objects will immediately redirect to the state defined in
# the alt_direct_transition field
physiology.state.enabled = true

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"

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

• Smith2004_CVS_human
• Guyton1972_PulmonaryOxygenIntake
• Guyton1972_PulmonaryFluidDynamics
• Lai2007_O2_Transport_Metabolism
• Brännmark2013 - Insulin signalling in human adipocytes (normal condition)
• Brännmark2013 - Insulin signalling in human adipocytes (diabetic condition)
• Talemi2015 - Persistent telomere-associated DNA damage foci (TAF)
• ChowHall2008 Dynamics of Human Weight Change_ODE_1
• Hong2009_CircadianClock
• Brown1997 - Plasma Melatonin Levels
• Leloup2004 - Mammalian Circadian Rhythm models for 23.8 and 24.2 hours
• Roblitz2013 - Menstrual Cycle following GnRH analogue administration
• Kyrylov2005_HPAaxis
• Jerby2010_Liver_Metabolism

[codecov]

Codecov Report

Merging #1391 (b448614) into master (9f7c6cc) will increase coverage by 0%.
Report is 15 commits behind head on master.
The diff coverage is n/a.

@@            Coverage Diff            @@
##             master   #1391    +/-   ##
=========================================
  Coverage        77%     77%            
- Complexity     3728    3790    +62     
=========================================
  Files           170     170            
  Lines         23981   24356   +375     
  Branches       3325    3442   +117     
=========================================
+ Hits          18654   18974   +320     
- Misses         4314    4346    +32     
- Partials       1013    1036    +23     

see 20 files with indirect coverage changes

📣 Codecov offers a browser extension for seamless coverage viewing on GitHub. Try it in Chrome or Firefox today!

[awatson1978]

Closing in favor of #1347