Biology Reference
In-Depth Information
vided. The module can export one CSML model into one simulation model with Java, FORTRAN,
C++, C, Perl or Python. The exported program can be directly compiled and executed with suitable
compiler of each programming language,
e.g.
, javac, gfortran95, g++, gcc or executed without the step
of compile,
i.e.
, Perl or Python. If the written script of the input model only contains predefined kinetics,
i.e.
, mass, stochasticmass, stochasticlognormalmass, Michaelis Menten provided in CIO 4.0 or using
custom kinetics, i. e. connectorrate, connectorcustom and custom, but limited to use four arithmetic op-
erations, IfTime(simulator, compare time), getElapsedTime(simulator), getSamplingInterval(simulator)
and ternary operator,
e.g.
, ? x : y;, then the generated model can be compiled without any updates (note
that the ternary operator is special scripting syntax for modules (3) and (4), this can be used instead of
“if” and “else” statement in normal simulation mode since if else syntax is supported in Pnuts script). In
other words, if the model contains other advanced syntax in Pnuts script language, the exported model
should apply custom update with some efforts. The exported result of the CSML model to several
programming languages is shown in Fig. 12. The function of this module to export with Java is used in
one of the processing steps in module “Pathway Parameter Search”.
CSML to SVG Module and CSML to HTML Module
In CIO 4.0, without using module functionalities, the model can be saved with some raster image
formats,
i.e.
, png or jpeg format, which are usually used for displaying purpose only. For editing
purpose, vector image format is better,
e.g.
, pdf, ai and SVG [50]. “CSML to SVG Module” is developed
for this purpose and can export the CSML model as a file with SVG format. The reason to select SVG
format among those vector image formats is that the format is the sole XML format to represent vector
image and also officially supported as a vector image format in CSML 3.0,
e.g.
<
image format="svg"
>
.
With the same reason all predefined biological terms with icons in CSML 3.0 are distributed in SVG
format. Many viewers and editors of SVG format are distributed,
e.g.
, Inkscape [51], Adobe Illustrator,
and CorelDraw, still with minor implementation differences of SVG format among them. Thus, the
exported result by this module might not be correctly displayed on some platforms and therefore the
module is currently in beta status. A snapshot of CIO 4.0 for the circadian rhythms in a
Mus musculus
model and the exported and loaded result on Inkscape are shown in Fig. 13.
For reporting purposes of CSML models, the “CSML to HTML Module” is provided. As in Fig. 14,
this module generates HTML files with png images by taking one CSML model as its input.
RESULTS AND DISCUSSION
Since the first release of Cell Illustrator 1.0, many developments and improvements have been made.
First, the native format is extended to be more suitable for biological pathway modeling, visualization,
and simulation of ontology background by using new formats CSML 3.0 and CSO 3.0. The CSML
3.0 can create simulation models not only limited to Petri net models but also ODE based models. The
standard icons are prepared in CSO 3.0 and thus user can create the graphical pathway model with
ontology background by simply preparing the D&D operations from the Biological Element dialog that
provides all those predefined icons. The created model becomes a template ready-for-simulation model
since it is represented with HFPNe. With the highly optimized feature of CSML 3.0 and CSO 3.0 to
represent biopathways, pathway databases in other formats can be imported to CIO 4.0 directly without
loss of any information,
e.g.
, KEGG, Reactome [39] with BioPAX [26], CellML repository [28], or
BioModels [52].
