SBML document import
You can import SBML model in jinkō. The the document to upload must be a valid SBML file.
Supported SBML versions
Jinkō supports all SBML versions up to SBML L3V2 which is the latest to date[1].
Imports in L3V2 are preferred since this version is natively supported in jinkō while SBML models in older format first undergo internally a conversion step to L3V2 before being processed.
Supported features
jinkō supports most of the SBML L3V2 core specifications:
| SBML core component | Supported in jinkō |
|---|---|
| Mathematical formulas | ✅* |
| Function definitions | ✅ |
| Unit definitions | ✅ |
| Compartments | ✅ |
| Species | ✅ |
| Parameters | ✅ |
| Initial assignments | ✅ |
| Rules | ✅* |
| Constraints | ❌ |
| Reactions | ✅ |
| Events | ✅ |
*in particular for the following components:
| SBML sub-component | Category | Supported in jinkō |
|---|---|---|
| 1. lambda expression | MathML node | ❌ |
| 2. delay | MathML node | ✅ |
| 3. quotient | MathML arithmetic operator | ❌ |
| 4. rateOf | MathML csymbol | ✅ |
| 5. Algebraic rule | Rule | ✅ |
Time unit
jinkō now supports other time units than second that are homogeneous to a time (hour, minute, day, etc.). Even though the SBML specifications permit it, jinkō does not yet support dimensionless time units.
Supported packages
The SBML standard specifies packages in addition to the core features. This is the list of currently supported packages:
| SBML package | SBML package nickname | Supported in jinkō |
|---|---|---|
| Arrays | arrays | ❌ |
| Hierarchical Model Composition | comp | ❌ |
| Distributions | distrib | ❌ |
| Dynamic Structures | dyn | ❌ |
| Flux Balance Constraints | fbc | ❌ |
| Layout | layout | ❌ |
| Extended MathML | math | ❌ |
| Multistate, Multicomponent and Multicompartment Species | multi | ❌ |
| Qualitative Models | qual | ❌ |
| Rendering | render | ❌ |
| Spatial Processes | spatial | ❌ |
Uploading an SBML document that relies on one or more unsupported packages will lead to an error notified to the end user (in both Jinko.ai and simwork).
1. as of 2022-05-03 ↩︎