Biology Reference
In-Depth Information
Fig. 4. Layout result of the ASE cell fate model in
C. elegans
. computed with the grid graph layout algorithm (SCCB) from a
random layout shown at the left-bottom. The model has 76 nodes (entities: 24; processes: 52) and 82 connectors.
up with their own XML formats. Therefore, development of XML with high expressive power that can
cover most of them for data import without loss of information while keeping their contents,
e.g.
, the
biological meanings, simulation model, and layout information, is important. To deal with this situation,
CSML version 3.0 [8] was developed as a highly optimized XML format for biopathway modeling and
simulation that almost achieves this objective (the latest version is 3.0 in September 2009). Its major
features are as follows:
1. Full compatibility with the pathway modeling and simulation ontology format Cell System Ontology
3.0 (CSO) [9].
With this feature, it is possible to exchange other ontology based formats,
e.g.
,
BioPAX [26].
2. Ability to contain the fact-based information that has no effect on the simulation model but has
very important meaning to the biopathway,
e.g.
, indirect regulation from one gene to another.
3. Capacity to represent not only high-level Petri net models but also ODE based models.
Cell Illustrator 4.0 faithfully implements the major CSML 3.0 specifications: other modeling and
simulation XML formats, such as SBML [27] and CellML [28], can be imported exactly into Cell
Illustrator 4.0. BioPAX can also be imported into Cell Illustrator 4.0 via CSO 3.0 format while com-
plementing kinetics to template simulation models. Other pathway databases,
e.g.
, KEGG [29,30] and
