Biology Reference
In-Depth Information
Table 1
URLs and options for CIO Application by Java Web Start
(a) Base URLs
Usage
Application
URL
Academic
CIO Player
CIO
Commercial
CIO Player
CIO
(b) Allowed options (suffixes)
Option
Allowed value
Status
Default
Note
required - Usually, .csml, .csml.gz, .cil or .cil.gz will be the suffix; it
is possible to specify multiple CSML models with “,”.
antialias on or off optional - If this value is on/off, then force apply antialias/non-
antialias to the displayed image; when this option is not
given, it starts without changing the setting of CIO.
mode GN or BP optional - If GN then CIO is forced to launch in gene network mode;
if BP then CIO is forced to launch in Petri net mode.
When this option is not given, it starts without changing
the setting of CIO.
XMX
integer value
optional 512 The value specifies the maximum memory (MB) of the
launched application. If the large gene network model
should be loaded on CIO. The size should be larger. In
32bit machine the maximum value can be 1400; in 64bit
machine, the maximum value will be almost unlimited.
(a) Select server and Java Web Start application. (b) Options for applications. If a model is located at http://www.aaa.
bbb/file.csml, user can make URL https://cionline.hgc.jp/cifileserver/launchCIOPlayer?model=http://www.aaa.bbb/file.csml
and can view the model in file.csml with CIO Player.
model
https://xxx/xxx.csml
or http://xxx/xxx.csml
Fig. 7. CIO Player is replaying the simulation of circadian rhythms in the
Drosophila melanogaster
model. CIO Play-
er can replay the simulation by loading the CIL file, a CSML file with log information. This image contains the load-
