Biology Reference
In-Depth Information
are interested in developing their skills for building biological pathways with Cell Illustrator.
The forthcoming Cell Illustrator Online (CIO 5.0) will have the full implementation of CSML 3.0. By
this feature, an entity-fact based pathway model (static pathway) and an entity-process based pathway
model (simulatable pathway) can be mixed into one model. The CIO 4.0 needs to model the entity-fact
and entity-process based pathway models in different modes, named “gene network mode” and “normal
mode”. Moreover, the user can create multiple sub-views from the main model by filtering the contents
with some rules,
e.g.
, gene layer, protein layer, nucleus layer, cytoplasmic layer, or expression levels
of each element. Those sub-views do not have any effect on simulation since the main model (model
before filtering) is simulated. Since the network size is getting larger,
e.g.
, several thousand elements,
the sub-view concept will be inevitable to grasp the characteristic features of those pathways.
In CSML 3.0, any language can be set for simulation of each kinetics and initial value, namely,
<
script
language=""
>
is used in that format. However, CIO 4.0 currently supports only the Pnuts language [44].
In CIO 5.0, script-based languages Javascript and Jython [54] and a compile-based Java language will
be allowed. Furthermore, CIO 5.0 will allow mixing of several script languages in one model,
e.g.
, one
reaction speed uses Javascript language and another reaction speed uses Java language. In CIO 4.0,
the simulation result of ODE compatible modeling as mentioned before (just model with continuous
elements and assign “nocheck” as the weight parameter of arcs) is similar to the simulation result of the
numerical integration of the Euler method. To keep better compatibility with the high precision ODE-
based simulators without violating the Petri-net formalism, higher order numerical integration methods,
e.g.
, Runge-Kutta, can be selected in the next release.
In CIO 4.0, the biological elements of mRNA, protein, and their modified form and complexes are
available as standard 92 icons of the CSO core vocabulary and 100,000 icons of the “CSMLDB Search
Module”. But CIO 4.0 supports less vocabulary of chemical compounds and the future release should
cope with this weakness owing to high user demand.
ACKNOWLEDGEMENTS
We are grateful to many people. First and foremost, we would like to thank the current and former
members of the Cell System Markup Language projects: Hiroko Nishihata, Kazuyuki Numata, Atsushi
Doi, Yayoi Sekiya, Yoshinori Tamada, Simamura Teppei, Ruy Yamaguchi, Seiya Imoto, Kazuko Ueno
of Human Genome Center in University of Tokyo; Hanji Hioka, Yuto Ikegami, Hironori Kitakaze,
Yoshimasa Miwa, Daichi Saihara, Tomoaki Yamamotoya, Hiroshi Matsuno of Yamaguchi University.
We would also thank users of Cell Illustrator who develop the excellent models on this platform and give
insightful feedbacks for the development of Cell Illustrator.
REFERENCES
[1]
Nagasaki, M., Doi, A., Matsuno, H. and Miyano, S. (2003). Genomic Object Net:
I. A platform for modeling and
simulating biopathways. Appl. Bioinformatics
2
, 181-184.
[2]
[3]
[4]
Kato, M., Nagasaki, M., Doi, A. and Miyano, S. (2005). Automatic drawing of biological networks using cross cost and
subcomponent data. Genome Inform.
16
, 22-31.
[5]
Kojima, K., Nagasaki, M., Jeong, E., Kato, M. and Miyano, S. (2007). An efficient grid layout algorithm for biological
networks utilizing various biological attributes. BMC Bioinformatics
8
, 76.
