Systems Biology Markup Language - Level 1

Herbert Sauro h*sauro at cds.cal*tech.edu
Mon Apr 23 18:43:42 EST 2001


We would like to announce the release of the final specification for Level 1
of SBML (the Systems Biology Markup Language). It is available from

http://www.cds.caltech.edu/erato

SBML is a description language for simulations in systems biology. It is
oriented towards representing biochemical networks that are common in
research on a number of topics, including cell signaling pathways, metabolic
pathways, biochemical reactions, gene regulation, and many others. SBML is
the product of close collaboration between the teams developing BioSpice
(http://gobi.lbl.gov/~aparkin/), Gepasi (http://www.gepasi.org/), DBSolve
(http://websites.ntl.com/~igor.goryanin/), E-Cell http://www.e-cell.org/),
Jarnac (http://members.tripod.co.uk/sauro/Jarnac.htm), StochSim
(http://www.zoo.cam.ac.uk/comp-cell/StochSim.html), and Virtual Cell
(http://www.nrcam.uchc.edu/).

The motivations for developing SBML stem from the current inability to
exchange models between biochemical network simulation/analysis tools. The
lack of a common standard for exchanging models poses two problems for
researchers.

First, models cannot be shared directly between tools because the file
format used by each tool is unique and nontransferable. This makes it
difficult if not impossible for a researcher to exchange models. Second,
when a simulator is upgraded or is no longer supported, models developed in
the `old' system become stranded and unusable in any other simulator. This
later scenario has already happened on a number of occasions, with the
resulting loss of the model to the scientific community. With the recent
roliferation of new biochemical simulators, this situation can only get
worse.

We have kept the base definition of SBML as simple as possible, so that
simulator developers will not find it too difficult to implement support for
SBML in their tools.

This base definition, called SBML Level 1, is the result of merging
modeling-language features from a number of existing software packages, and
encompasses the minimal information required for biochemical models.
Additional structures and facilities will be added to SBML in subsequent
levels; among the features we are developing for SBML Level 2 are
hierarchical models and spatial characteristics. By freezing subsets of
features in SBML definitions at incremental levels, we hope to provide the
community with stable standards to which software authors can design to,
while at the same time allowing the simulation community to gain experience
with the language definitions before introducing new elements.

The effort perhaps closest in spirit to SBML is CellML

(http://www.cellml.org). CellML is an XML-based markup language designed for
storing and exchanging computer-based biological models. The constructs in
CellML tend to be at a more abstract and general level than those in SBML
Level 1, and describe the structure and underlying mathematics of cellular
models in a very general way. By contrast, SBML is closer to the internal
object model used in model analysissoftware. Because SBML Level 1 is being
developed in the context of interacting with a number of existing simulation
packages, it is a more concrete language than CellML and may be better
suited to its purpose of enabling interoperability with existing simulation
tools. However, CellML offers viable alternative ideas, and the developers
of SBML and CellML are actively engaged in ensuring that the two
representations can be translated between each other.






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