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Hi All,

A friend of mine noticed this at PSB this year and I thought others
might find it interesting.

Thanks.

Ben


CSML 1.9: Biopathway Modeling and Simulation Markup Langage
Masao Nagasaki, Atsushi Doi and Satoru Miyano

Around 1999, there was no practically usable software tool for
biological pathway modeling and simulation. However, currently,
there have been appearing some software tools which are
end-usable in practice to some extent. Furthermore, some pathway
databases are commercially available though they provide only
static models. Their software tools and pathway databases have
merits and demerits of their own. Thus, from users' viewpoint,
the issue of resource exchanges between software tools and
pathway databases are based on some XML formats. Especially
CellML v 1.0 and SBML v 1.0 have been making progress towards
standardization of biological system desription for simulation.
In the beginning of discussions around 2000, there was a
criticism that SBML has only the ability to desribe 9% of GEPASI
that compiles kinetics information of metabolic pathways. After
CSML v. 2 was released in 2003, more than 50 software tools such
as SBW, CellDesigner, Virtual Cell, Cellware, Dizzy, CADLINE show
their interest to support SBML in their products. However, due
to the process of standardization, the current version of SBML
requires more improvements in its discriptional ability to
achieve a high level of customer (biologist) satisfaction. In
fact, both CellML and SBML are wweak with respect to the
description functions for visualization of biologists to
understand and analyze biological pathways though they can
describe static and dynamic features in pathways to some
extent. With the history and background, in the process of
developing Cell Illustrator, we have been developing an XML
called Cell System Markkup Language (CSML) for describing
biological pathways which also comprehensively supports SBML and
CellML by adopting the HFPNe architecture for description of
dynamics. The XML format fo CSML v 1.9 consists of the following
five kinds of information, knowledge and data:

1) static structure,
2) dynamics,
3) biological graphical image,
4) biological annotation, and
4) simulation result.

The details are available from http://www.csml.org/. With the
development of CSML v 1.9, conversion software SBML and CellML to
CSML are also created so that all models in SBML and CellML can
be run on CSML v 1.9 software environment, e.g. Cell Illustrator.
As the demonstration, we apply the software to some pathway
models in BioModels that stores biopathway models with SBML
format and execute the modle on Cell Illustrator for its
usability.