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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
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Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species,
Fengkai Zhang1, Lucian P Smith2, Michael L Blinov3
1NIAID/NIH, Bethesda, USA.
Journal of Integrative Bioinformatics
|July 7, 2020
Summary
Rule-based modeling simplifies complex biological systems by defining molecular interactions through rules. The Systems Biology Markup Language (SBML) Level 3 Multi Package standardizes these rule-based models for easier sharing and analysis.
Area of Science:
- Systems Biology
- Computational Biology
- Biochemical Modeling
Background:
- Rule-based modeling offers a powerful approach to construct complex reaction networks by specifying rules for molecular interactions.
- This method allows for detailed specification of sub-molecular domains, component states, binding status, and spatial information.
- The use of 'wildcards' enables the definition of entire families of molecule complexes as patterns, simplifying models with multiple components, states, and compartments.
Purpose of the Study:
- To provide the specification for Release 2 of Version 1 of the Systems Biology Markup Language (SBML) Level 3 Multi package.
- To detail the extension of the SBML Level 3 core with the 'type' concept for Species and Compartment classes, enabling pattern-based species and multi-location existence.
- To document minor corrections and clarifications without altering the core model description.
Main Methods:
- Specification document for the SBML Level 3 Multi package, Release 2 of Version 1.
- Extension of SBML Level 3 Version 1 core by incorporating the 'type' concept into Species and Compartment classes.
- Description of how reaction rules can incorporate species patterns and multiple locations.
Main Results:
- The SBML Level 3 Multi Package Version 1 (Release 2) extends SBML capabilities to support rule-based modeling with enhanced pattern matching and spatial information.
- This standard facilitates the definition of complex biological models involving numerous species, states, and compartments.
- Software tools like Simmune and BioNetGen support this standard, promoting interoperability of rule-based models.
Conclusions:
- The SBML Level 3 Multi Package provides a standardized format for rule-based modeling in systems biology.
- This specification enhances the ability to represent and exchange complex biochemical models, fostering collaborative research.
- Release 2 focuses on errata correction and clarification, ensuring the stability and usability of the standard.
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