SBML (file format)

File format title

SBML

Element type

diagram

Plugin

biouml.plugins.sbml (Support for SBML models)

SBML format

The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard which can represent many different classes of biological phenomena, including metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others.

BioUML allows to represent SBML models using the Systems Biology Graphical Notation (SBGN).

SBML structure

A model definition in SBML Levels 3 Version 1 consists of lists of the following components.

• Function definition: A named mathematical function that may be used throughout the rest of a model.
• Unit definition: A named definition of a new unit of measurement. Named units can be used in the expression of quantities in a model.
• Compartment: A well-stirred container of finite size where species may be located. Compartments may or may not represent actual physical structures.
• Species: A pool of entities of the same kind located in a compartment and participating in reactions (processes). In biochemical network models, common examples of species include ions, proteins and other molecules; however, in practice, an SBML species can be any kind of entity that makes sense in the context of a given model.
• Parameter: A quantity with a symbolic name. In SBML, the term parameter is used in a generic sense to refer to named quantities regardless of whether they are constants or variables in a model. SBML Level 3 provides the ability to define parameters that are global to a model as well as parameters that are local to a single reaction.
• Initial Assignment: A mathematical expression used to determine the initial conditions of a model. This type of object can only be used to define how the value of a variable can be calculated from other values and variables at the start of simulated time.
• Rule: A mathematical expression added to the set of equations constructed based on the reactions defined in a model. Rules can be used to define how a variable's value can be calculated from other variables, or used to define the rate of change of a variable. The set of rules in a model can be used with the reaction rate equations to determine the behavior of the model with respect to time. Rules constrain the model for the entire duration of simulated time.
• Constraint: A means of detecting out-of-bounds conditions during a dynamical simulation and optionally issuing diagnostic messages. Constraints are defined by an arbitrary mathematical expression computing a true/false value from model variables, parameters and constants. An SBML constraint applies at all instants of simulated time; however, the set of constraints in model should not be used to determine the behavior of the model with respect to time.
• Reaction: A statement describing some transformation, transport or binding process that can change the amount of one or more species. For example, a reaction may describe how certain entities (reactants) are transformed into certain other entities (products). Reactions have associated kinetic rate expressions describing how quickly they take place.
• Event: A statement describing an instantaneous, discontinuous change in one or more variables of any type (species, compartment, parameter, etc.) when a triggering condition is satisfied.

Supported formats

• SBML level 1 version 1
• SBML level 1 version 2
• SBML level 2 version 1
• SBML level 2 version 2
• SBML level 2 version 3
• SBML level 2 version 4
• SBML level 3 version 1

References

1. http://sbml.org/
2. http://en.wikipedia.org/wiki/SBML