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.

SimBiology XLSX

You can export a computational model as an XLSX workbook that can be imported in SimBiology. The export bundle also includes the simulation settings derived from Jinkō's solving options.

Jinkō adapts model constructs to the SimBiology XLSX representation when their formats or semantics differ. These adaptations can add new modeling components, such as rules, parameters, reactions, events or doses. The table below describes the resulting workbook changes, so you can review the generated export before using it in SimBiology.

Jinkō feature or behavior	SimBiology representation	Jinkō export adaptation
Categorical parameters and case expressions	No direct support for categorical parameters and case expressions.	Formulas are resolved using the model's selected categorical values before creating the workbook. The XLSX workbook contains resolved formulas rather than editable categorical choices.
Unit annotations in formulas	No direct support for unit annotations.	The exporter creates constant auxiliary parameters with a value of 1 for non-dimensionless unit annotations and updates formulas to refer to them.
Conditional expressions	No direct support for conditional expressions.	Conditional expressions are rewritten into equivalent boolean-weighted formulas.
Species referenced in formulas	Species referenced in formulas are considered to be in their initial amount unit.1	The exporter converts initial conditions to the model's extent units. This aligns the units used for species references in Jinkō and SimBiology.
Non-constant parameter and compartment values	Values are calculated by assignment rules instead of being stored directly in the Parameters or Compartments sheet.	The exporter creates initial-assignment rules for constant parameters and parameters driven by an ODE or event, repeated-assignment rules for other parameters and compartments.
Conditional filters on reactions, ODEs, and algebraic rules	The XLSX workbook contains a static active state for each component.	The exporter evaluates filters that can be resolved statically. When a filter cannot be resolved statically, the exported component is marked active.
Reactions with variable stoichiometry	No support for variable stoichiometry.	Reactions with variable stoichiometry are split into atomic reactions with only one reactant or product, and adjusted rates that include variable stoichiometric coefficients.
Time-based events	Under specific conditions, time-based events can be represented as scheduled doses or repeat doses. Those conditions include: time-based events that target species, that do not have a condition, whose update is an increment, and whose recurrence parameters are either constant or a direct reference to a model parameter.	The exporter converts eligible events to doses with the corresponding target species and dose amount. For other time-based events, the exporter creates self-rearming root-based events with auxiliary parameters that track the next trigger time and when needed the occurrence count.

Footnotes

1. This conversion depends on the unit-checking mode. With UnitCheckAndConvertOnlyReactantsAndProductsToExtentUnit, species that are not reactants or products retain their initial condition units when referenced in formulas. ↩