(Strictly Private) 2007/1/10

Please select a link from the following list,
which is linked to a model opened by Java Web Start version of CellDesigner.
Some models are ready for simulation.

• MAPK
• simulation
• database access
• Kitano-TLR-Fig1
• Cell Division Cycle
• Signal Transduction and Carbohydrate Metabolic Pathways
• BIOMD0000000001
• BIOMD0000000002
• BIOMD0000000003
• BIOMD0000000004
• BIOMD0000000005
• BIOMD0000000006
• BIOMD0000000007
• BIOMD0000000008
• BIOMD0000000009
• BIOMD0000000010
• BIOMD0000000011
• BIOMD0000000012
• BIOMD0000000013
• BIOMD0000000014
• BIOMD0000000015
• BIOMD0000000016
• BIOMD0000000017
• BIOMD0000000018
• BIOMD0000000019
• BIOMD0000000020
• BIOMD0000000021
• BIOMD0000000022
• BIOMD0000000023
• BIOMD0000000024
• BIOMD0000000025
• BIOMD0000000026
• BIOMD0000000027
• BIOMD0000000028
• BIOMD0000000029
• BIOMD0000000030
• BIOMD0000000031
• BIOMD0000000032
• BIOMD0000000033
• BIOMD0000000034
• BIOMD0000000035
• BIOMD0000000036
• BIOMD0000000037
• BIOMD0000000038
• BIOMD0000000039
• BIOMD0000000040
• BIOMD0000000041
• BIOMD0000000042
• BIOMD0000000043
• BIOMD0000000044
• BIOMD0000000045
• BIOMD0000000046
• BIOMD0000000047
• BIOMD0000000048
• BIOMD0000000049
• BIOMD0000000050
• BIOMD0000000051
• BIOMD0000000052
• BIOMD0000000053
• BIOMD0000000054
• BIOMD0000000055
• BIOMD0000000056
• BIOMD0000000057
• BIOMD0000000058
• BIOMD0000000059
• BIOMD0000000060
• BIOMD0000000061
• BIOMD0000000062
• BIOMD0000000063
• BIOMD0000000064
• BIOMD0000000065
• BIOMD0000000066
• BIOMD0000000067
• BIOMD0000000068
• BIOMD0000000069
• BIOMD0000000070
• BIOMD0000000071
• BIOMD0000000072
• BIOMD0000000073
• BIOMD0000000074
• BIOMD0000000075
• BIOMD0000000076
• BIOMD0000000077
• BIOMD0000000078
• BIOMD0000000079
• BIOMD0000000080
• BIOMD0000000081
• BIOMD0000000082
• BIOMD0000000083
• BIOMD0000000084
• BIOMD0000000085
• BIOMD0000000086
• BIOMD0000000087

Here is a detailed information about Java Web Start version of CellDesigner.

[Simulation]

Please select [Simulation] -> [Control Panel] menu to execute a simulation.

[Auto Layout]

CellDesigner Java Web Start also supports new improved auto-layout algorithms.
Please select [Layout] -> [Organic], [Layout] -> [Hierarchic], [Layout] -> [Circular] menu
to change the layout of model (default is "Orthogonal" layout).

[Database access]

Once you have launched CellDesigner Java Web Start, you can import a model from BioModels.net database, using

[Database] -> [Import from Biomodels.net] menu.

Please select a model, and then press [Import] button.
Also, you can browse a reference publication and description of the model in your web browser
by pressing [Reference] and [Description] button.

[Supported OS]

CellDesigner Java Web Start uses native library to improve the performance of simulation.
Due to this fact, current beta version only supports Windows.
We have tested on WindowsXP SP2 and Windows2000 with JRE 1.5.
The release version of CellDesigner Java Web Start will support MacOSX and Linux.

The current version is a beta version, so there may have some problems and some missing features.
For example, following problems are known.
1. Some models in BioModels.net doesn't work on CellDesigner Java Web Start (I'm not sure this is a CellDesigner's problem, though).
2. [Layout] -> [Tree] menu doesn't work due to the current data structure of the model.

-- by Akira Funahashi, Ph.D. | Kitano Symbiotic Systems Project ERATO-SORST, JST | The Systems Biology Institute last updated 2006/7/19