Physiology Models (Borked)

[awatson1978]

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 #1254 (ab9c85c) into master (7a5348f) will increase coverage by 0%.
Report is 155 commits behind head on master.
The diff coverage is n/a.

❗ Current head ab9c85c differs from pull request most recent head 2e115c6. Consider uploading reports for the commit 2e115c6 to get more accurate results

@@            Coverage Diff             @@
##             master   #1254     +/-   ##
==========================================
  Coverage        78%     79%             
- Complexity     3635    3874    +239     
==========================================
  Files           167     167             
  Lines         23659   24941   +1282     
  Branches       3220    3566    +346     
==========================================
+ Hits          18643   19756   +1113     
- Misses         3996    4160    +164     
- Partials       1020    1025      +5     

see 27 files with indirect coverage changes

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[jawalonoski]

After a quick glance, here are a few quick thoughts:

• You probably want to remove all of the .idea/ files and add .idea/** to .gitignore.
• You also made some non-functional whitespace changes (some with trailing whitespace that our style guidelines will issue warnings about) that you probably should revert.
• You have *.bkup copies of files that you probably did not intend to commit that should probably be removed.

[jawalonoski]

Many of the wearable submodule files start with gallstones_* not sure if this is copy & paste or if you tied this to gallstones or what, but ideally these should be independent of gallstones. Let's discuss.

[sonatype-lift]

NULLPTR_DEREFERENCE: null (last assigned on line 776) is dereferenced.

❗❗ 2 similar findings have been found in this PR

🔎 Expand here to view all instances of this finding

File Path	Line Number
src/main/java/org/mitre/synthea/export/rif/CarrierExporter.java	69
src/main/java/org/mitre/synthea/export/rif/BeneficiaryExporter.java	487

Visit the Lift Web Console to find more details in your report.

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[sonatype-lift]

NULLPTR_DEREFERENCE: null (last assigned on line 777) is dereferenced.

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@sonatype-lift ignore	Leave out the above finding from this PR
@sonatype-lift ignoreall	Leave out all the existing findings from this PR
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[sonatype-lift]

🛠 Lift Auto-fix

Some of the Lift findings in this PR can be automatically fixed. You can download and apply these changes in your local project directory of your branch to review the suggestions before committing.¹

# Download the patch
curl https://lift.sonatype.com/api/patch/github.com/synthetichealth/synthea/1254.diff -o lift-autofixes.diff

# Apply the patch with git
git apply lift-autofixes.diff

# Review the changes
git diff

Want it all in a single command? Open a terminal in your project's directory and copy and paste the following command:

curl https://lift.sonatype.com/api/patch/github.com/synthetichealth/synthea/1254.diff | git apply

Once you're satisfied, commit and push your changes in your project.

Footnotes

1. You can preview the patch by opening the patch URL in the browser. ↩

[awatson1978]

Replaced by #1347