SBML

SBML stands for Systems Biology Markup Language. It is a model representation format for systems biology. SBML is built to descibe systems of biochemical reactions be it cell signaling pathways, metabolic pathways, gene regulatory networks and others. SBML is structured on XML (eXtensible Markup Language) and follows XML schema.

With rapidly evolving field of systems biology and various computational tools and techniques, a common format was required for "communication" between different tools and techniques. SBML tries to just that! Infact, SBML can be described as lingua franca of systems biology. A word of caution though SBML is not an attempt to define a universal language but to enable communication of most essential aspects of the models.

Structure of SBML:

A model is usually sum total of reactant and product species, reactions, reaction rates amd parameters of rate expression, compartments of the species and units. In SBML, each component is described using a specific type of data object that organizes the relevant information:

beginning of model definition
list of funtion definitions (optional)
list of unit definions (optional)
list of compartment types (optional)
list of species types (optional)
list of compartments (optional)
list of species (optional)
list of parameters (optional)
list of initial assignments (optional)
list of rules (optional)
list of constraints (optional)
list of reactions (optional)
list of events (optional)
end of model definition

The explanation of each component taken from SBML documentation is given below:

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, or a redefinition of an SBML predefined unit. Named units can be used in the expression of quantities in a model.

Compartment Type: A type of location where reacting entities such as chemical substances may be located.

Species type: A type of entity that can participate in reactions. Typical examples of species types include ions such as Ca2+, molecules such as glucose or ATP, and more.

Compartment: A well-stirred container of a particular type and finite size where species may be located. A model may contain multiple compartments of the same compartment type. Every species in a model must be located in a compartment.

Species: A pool of entities of the same species type located in a specific compartment.

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 2 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. The set of rules constrains 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 a set of variables of any type (species quantity, compartment size or parameter value) when a triggering condition is satisfied.

A software tool can read SBML and translate it into its own format for model analysis. The tool can then used for networking the model or smilulating the model by constructing differential equations representing the network and then perform numerical time integration on the equations to explore the model's dynamic behaviour.

Further infromation can be found at http://sbml.org/.