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Example models missing parameter values/distributions, rate laws, observables, and state initial values #62

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SamWitty opened this issue Oct 25, 2023 · 2 comments
Open
20 of 40 tasks

Example models missing parameter values/distributions, rate laws, observables, and state initial values #62

SamWitty opened this issue Oct 25, 2023 · 2 comments
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@djinnome @JosephCottam
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bug Something isn't working discussion examples integration

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@SamWitty
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SamWitty commented Oct 25, 2023 •
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A fully specified AMR should contain all of the following components:

  • Parameter values/distributions
  • Rate laws expressions
  • Observables (Optional)
  • State Initial values

Currently, none of the examples in this repository contain all 4 of these components. The following list summarizes my current accounting of which models contain which components. Completion of this issue will involve updating each example accordingly.

Parameter values/distributions

  • petrinet/flux_typed
  • petrinet/flux_typed_aug
  • petrinet/ont_pop_vax
  • petrinet/sir
  • petrinet/sir_flux_span
  • petrinet/sir_typed
  • petrinet/sir_typed_aug
  • regnet/lotka_volterra
  • regnet/syntax_edge_cases
  • stockflow/sir

Rate Law expressions

  • petrinet/flux_typed
  • petrinet/flux_typed_aug
  • petrinet/ont_pop_vax
  • petrinet/sir
  • petrinet/sir_flux_span
  • petrinet/sir_typed
  • petrinet/sir_typed_aug
  • regnet/lotka_volterra
  • regnet/syntax_edge_cases
  • stockflow/sir

Observables

  • petrinet/flux_typed
  • petrinet/flux_typed_aug
  • petrinet/ont_pop_vax
  • petrinet/sir
  • petrinet/sir_flux_span
  • petrinet/sir_typed
  • petrinet/sir_typed_aug
  • regnet/lotka_volterra
  • regnet/syntax_edge_cases
  • stockflow/sir

State initial values

  • petrinet/flux_typed
  • petrinet/flux_typed_aug
  • petrinet/ont_pop_vax
  • petrinet/sir
  • petrinet/sir_flux_span
  • petrinet/sir_typed
  • petrinet/sir_typed_aug
  • regnet/lotka_volterra
  • regnet/syntax_edge_cases
  • stockflow/sir
@SamWitty SamWitty mentioned this issue Oct 25, 2023
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@JosephCottam
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Model-checker (draft) now available in https://github.com/ciemss/Model-Representations/tree/jc-model-checks

Tries to compute the checkmarks @SamWitty listed above. Run as python validation/model_inventory.py petrinet/examples/*.json.

@SamWitty -- Does this checking make sense? Right now it looks at both pdeandodeinsemantics`, but I don't know if that is the right thing (I only have a few examples to go off of).

@djinnome -- The check_schema function validation/model_inventory.py is what I plan to use as the filter for my model-loading function.

@SamWitty
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SamWitty commented Nov 16, 2023 •
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@JosephCottam, sorry I missed this message. I never received an email notification for some reason, which usually happens ...

These checks looks great. Could you make a PR to this repo? I'd recommend assigning @bgyori as a reviewer.

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@JosephCottam JosephCottam

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62-example-models-missing-parameter-valuesdistributions-rate-laws-observables-and-state-initial-values ciemss/Model-Representations
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@djinnome @JosephCottam @SamWitty