Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1.

Area of Science:

• Systems biology
• Computational biology
• Bioinformatics

Background:

• Biological models frequently incorporate parameters with inherent uncertainty or stochastic origins.
• Current Systems Biology Markup Language (SBML) Level 3 Core lacks direct support for representing inexact numerical values.
• The extensibility of SBML via packages offers a pathway to address limitations in the Core specification.

Purpose of the Study:

• To introduce a mechanism for representing inexact and stochastic values within biological models.
• To extend the Systems Biology Markup Language (SBML) Level 3 Core specification.
• To enable the encoding of value distributions and uncertainty in computational models.

Main Methods:

• Leveraging the SBML package mechanism for extending the Core specification.
• Developing and integrating the SBML Distributions package.
• Implementing syntactic constructs to represent probability distributions and uncertainty.

Main Results:

• The SBML Distributions package successfully extends SBML Level 3.
• Models can now explicitly encode information about the distribution and uncertainty of parameter values.
• Facilitates more accurate representation of stochastic and uncertain biological systems.

Conclusions:

• The SBML Distributions package enhances the capability of SBML for modeling biological systems with inherent uncertainty.
• This extension supports more robust and realistic computational modeling in systems biology.
• Enables better integration of stochastic data into standardized biological model descriptions.