SBML export

SBML standard is a key medium for exchanging models in systems biology. However, encoding rule-based, domain-detailed models using the concepts of Species and Compartment in SBML can be difficult for models with complex rules that lead to large numbers of particular reactions. For that, SBML Level 3 package: Multistate, Multicomponent and Multicompartment Species extends the SBML Level 3 core with the “type” concept in the Species and Compartment classes and therefore reaction rules may contain species that can be patterns and be in multiple locations in reaction rules. It allows SBML standard for encoding rule-based models using their “native” concepts for describing reactions instead of having to apply the rules and unfold the networks prior to encoding in an SBML format.

This tool allows to export a BCSL model in SBML format supporting the multi package.

A step by step Galaxy tour showing how to use the tool can be found here.

Input specification

• Model file: Selected model in BCSL language (see Model syntax for details).

Output specification

The results of the tool is an XML file containing equivalent model in SBML format.

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Command line arguments

usage: ExportSBML.py [-h] --model MODEL --output OUTPUT

Export SBML model with usage of SBML-multi package

required arguments:
  --model MODEL
  --output OUTPUT