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Exporting computational models from jinkō

You can download computational models from jinkō in several formats.

In the app, this option is available at the bottom of the Info section in the right-side panel when you are in a computational model (CM).

You can also export a model through the API route /core/v2/model_manager/jinko_model/{coreItemId}/snapshots/{snapshotId}/bundle, as documented in the API reference.

SBML​

SBML is the standard format for representing biological models. It is widely used in systems biology and supported by many software tools.

All versions from L1V1 to L3V2 are supported. If you plan to use the model in SimBiology, we recommend exporting to L2V4.

SimBiology can have issues with large SBML models, so we cannot guarantee that exports will work immediately without adjustments.

Some advanced jinkō modeling options may not be represented faithfully, including:

  • Categorical parameters will be inlined using the model's default values
  • Some bioreactions will be converted to simple ODEs

JSON​

JSON is a lightweight data-interchange format that is easy for humans to read and write, and easy for machines to parse and generate.

You can export the differential model in JSON format. This is useful when you want to inspect aggregated equations per species, or identify parameters involved in the left-hand side of equations (for example, when species are involved across several reactions).

The JSON format exposes jinkō's internal representation and may change at any time without notice. We generally maintain backward compatibility for a few months. Importing and re-exporting your model upgrades it to the latest schema version.

This is the recommended format because it is the only one that preserves all model information. For long-term archival, however, we recommend SBML.

Julia DifferentialEquations.jl (beta)​

Julia is a high-level, high-performance dynamic language for numerical computing.

DifferentialEquations.jl is a Julia interface to ODE solvers.

We export a self-contained Julia program that includes the model definition, a DifferentialEquations.jl solver call, and basic support for data visualization.

Some jinkō features are not yet supported in Julia:

  • Algebraic equations
  • Delays
  • Advanced events (such as time-based events with conditions, delays, and priorities)

Advanced jinkō modeling options may not be faithfully represented, including:

  • Categorical parameters will be inlined using the model's default values
  • All bioreactions will be converted to simple ODEs
  • Event definitions are flattened (for example, recurring events are turned into an explicit listing of all event occurrences)
  • The accuracy of results produced by this executable is not guaranteed because of differences in internal solver behavior.

This is the recommended format if you are familiar with Julia/DifferentialEquations.jl and want to run locally a model designed in jinkō. You will likely need to adapt the self-contained executable to your requirements.

Please let us know if you need improvements to this feature.

R nlmixr2/rxode2​

We export a self-contained R program that includes the model definition, an nlmixr2/rxode2 solver call, and basic support for data visualization.

Some jinkō features are not yet supported:

  • Algebraic equations
  • Delays
  • Events

Advanced jinkō modeling options may not be faithfully represented, including:

  • Categorical parameters will be inlined using the model's default values
  • All bioreactions will be converted to simple ODEs
  • The accuracy of results produced by this executable is not guaranteed because of differences in internal solver behavior.

This is the recommended format if you are familiar with R/nlmixr2/rxode2 and want to run locally a model designed in jinkō. You will likely need to adapt the self-contained executable to your requirements.

Please let us know if you need improvements to this feature.

Not supported yet: XLSX (SimBiology-compliant spreadsheets)​

Please let us know if you need this feature.