0

Import an SBML document in jinkō

  • updated 4 mths ago

You can import SBML models in jinkō following the same instructions as in here except that the document to upload is 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 ❌

A consequence of 5. is that jinkō does not yet support Differential-Algebraic Equations (DAE).

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 ↩

Reply Oldest first
  • Oldest first
  • Newest first
  • Active threads
  • Popular