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The source code of the engine generated by SECG can be exported to file in
Java or other languages. The source code file can then be edited, which allows for
better control over the simulation. Also the simulation source code can be controlled
and executed in other program, which is useful for performing parameter
optimization, or generating some advanced statistics from the engine run.
The exact reference for advanced usage, which contains description how the
SECG framework works and detailed information of the content of each source code
file is obtainable from Masao Nagasaki ([email protected] or check
http://www.csml.org).
Note: Profiting from the SECG engine possibilities to the full extent requires some
software development skills.
6.5
Remote Simulation Servers
In Cell Illustrator, simulations are normally executed at your desktop machine
using the default simulation engine which is tightly integrated with the remaining
program components. These local simulations are interactive, i.e., the canvas is
updated during the simulation run, and you may pause or move through the
simulation. However, you can neither edit another model nor run another simulation
in this mode. Thus, running simulations in your CI Workspace is recommended for
debugging purposes and simulations that are not time consuming. For large models
and lengthy simulations, sending a simulation job to a remote server is recommended.
The Cell Illustrator Server (CI Server) is a companion product of Cell Illustrator and
it is not a part of the standard CI package. Hence, this option is available only to
users who have additionally purchased the CI Server. One server can be accessed by
multiple users of the Cell Illustrator desktop package, or alternatively one can connect
to more than one CI Server from your desktop. The remote server mode of running
simulations is also useful if you intend to run many simulations in parallel. The server
mode of simulations does not drain upon the resources of your computer, so you may
continue to work with CI or other applications after submitting many simulations to a
server.
Technically, CI Server is a web service installed at an Apache Tomcat web
server. A remote simulation is completed in three steps: (1) upload the model input
file to the server, (2) execute the simulation using the engine installed at the server,
and (3) download the output file (Simulation Log). The CI Server installation
procedure requires the skills of an IT system administrator and is described in the Cell
Illustrator Server Installation Manual. Once the CI Server is installed, you need to
configure your CI Workspace to access it.
6.5.1
Registering a CI Server
To submit simulations to a server, you must add it to the list of servers in your
CI Workspace. For this, you will need to specify the URL address of the respective
web service. Optionally, if the web service is password protected, you will also need
to specify the authorization data (user name and password). . The menu command
Simulation | Setup Servers opens the Setup Servers dialog, in which you can view and
manage the list of servers. With the Test button you can confirm that the selected CI
Server is accessible.
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