SBML example models passes the online syntax validation that is available at http://
sbml.org/tools/htdocs/sbmltools.php, which prevents, for instance, the transfer of
models from JDesigner to CellDesigner.
Like all SBW-enabled programs, JDesigner has a special menu called SBW that
lists the services provided by other SBW modules. Services provided with the stan-
dard distribution are stochastic time course simulations, deterministic time course
and steady-state calculations, and the generation of a Matlab ODE function file of
the current model. However, JDesigner also offers another, tighter, integration with
Jarnac, a network simulation module. The menu entry “Actions/Connect Simulator”
establishes a direct connection to Jarnac, which in turn enables several entries in the
Analysis menu. The left side of Fig. 14.5 shows the control panel that appears if the
Time Course Simulation is chosen from this menu. After the simulation is finished,
a graphical representation of the solution can be examined (bottom of Fig. 14.5). The
graphical output is very flexible and allows selection of the variables to be plotted, of
the axes labels and scaling, and of titles and legends. Furthermore, the result can be
saved in different graphic formats and the numerical values can be exported as text,
XML, or Excel format. Finally, a good tutorial on how to use JDesigner is available
from http://public.kgi.edu/~hsauro/sysbio/papers/JDBooklet.pdf.
14.1.5.2 CellDesigner
CellDesigner, another network creation tool, might be an alternative to JDesigner for
people who do not use Microsoft Windows (Funahashi et al. 2003). The application
is written in Java and therefore also runs under MacOS X and Linux. The current
version is 2.0 and can be downloaded from http://systems-biology.org. As with JDe-
signer, networks can be constructed from compartments, species, and reactions.
However, CellDesigner comes with a large number of predefined shapes that can be
used for different types of molecules such as proteins, receptors, ion channels, small
metabolites, etc. It is also possible to modify the symbols to indicate phosphoryla-
tions or other modifications (Fig. 14.6, center). The program also provides several
icons for special reaction types such as catalysis, transport, inhibition, and activa-
tion.
Reading and writing of the models is SBML-based (Level 1 and 2), and the models
written by CellDesigner pass the online validation at http://sbml.org/tools/htdocs/
sbmltools.php and thus conform to the SBML standard. A nice feature in this re-
spect is the ability to display the SBML model structure as a tree (Fig. 14.6, left side).
A click on a species or reaction in this tree highlights the corresponding elements in
the graphics canvas and in the matching tab on the right side showing further de-
tails. This tab is also the place where initial concentrations and reaction details are
entered. Like JDesigner, CellDesigner allows entering arbitrary kinetic equations,
but unfortunately it has no list of standard kinetics (mass action or Michaelis-Men-
ten) that can be applied. For each reaction, the rate law has to be typed in by hand.
A connection to SBW is realized via the standard SBW menu and provides the ser-
vices described together with JDesigner. For a further introduction to CellDesigner, a
startup guide can be obtained from the download page at http://systems-biology.org.
431
14.1 Modeling and Visualization