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
- http://sbml.org/
- http://en.wikipedia.org/wiki/SBML