SYSTEMS BIOLOGY MARKUP LANGUAGE (SBML)
SBML is a machine-readable language, based on XML, free and open interchange
format for representing models of biological processes.
It can represent metabolic networks, cell-signaling pathways, regulatory networks
and many other kinds of systems.
SBML as an input and output format, different software tools can operate on the same
representation of a model, removing chances for errors in translation and assuring a
common starting point for analyses and simulations
SBML can encode models consisting of entities
(for example, molecular species) linked and modified
by processes (for example, biochemical reactions).
Here is an artificial example of a small set of biochemical reactions
The symbols in square brackets (e.g., S1) represent concentrations of molecular species,
the arrows represent reactions, and the formulas above the arrows represent the rates at
which the reactions take place.
Broken down into its constituents, this model contains a number of components: reactant
species, product species, reactions, reaction rates, and parameters in the rate expressions.
Two important principles in SBML are that
Models are decomposed into explicitly-labeled constituent elements, and
The representation deliberately does not cast the model directly into a set of differential
equations or other specific interpretation of the model.
This makes it easier for a software tool to interpret the model and translate the SBML form
into whatever internal form the tool actually uses
How is SBML is used?
• Meant to provide an exchange language for software tools
• Don’t write SBML by hand, a software can do it
• Software tools that “speak” SBML provides a higher-level interface
• Applications usually have their own native format.
• Import/export SBML rather than natively save as SBML.
Some important SBML constructs
Additional useful elements
Rules in SBML define extra mathematical expressions
E.g., If need to express additional mathematical
relationships beyond what is implied by the
system of reactions.
Rules that defines relationship that hold at all times
Rules in the context of the overall model
Equation derived from
(And while this example uses concentrations, it could equally have used other measures, such as the number of molecules of each chemical species.)
Accepted by dozens of journals
100’s of software tools available today
Libraries: libSBML, JSBML
260+ listed in SBML software guide
1000’s of model available
In public databases eg., Bio-Models database, Reactome
As supplementary data to papers
In private repositories
Level 3 packages add constructs on top of sbml level 3 core