the SimDriver jar file, is a very small front end that will enable you to perform timecourse simulations with various simulators. We wrote the application to provide access to the simulators for users that don't have access the the C# version of the program which is more powerful. But back to the Java version:
- to start it a simple double click on the Jar file should suffice.
Once the Application starts, a click on "Load Model" will enable you to load any sbml file. After that you specify the start and endpoint, as well as the number of output points you would like to see. Finally a click on simulate will simulate the model and plot the results.
Please let me know whether this worked for you.
thank you
best
Frank
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Just double clicking on SimDriver.jar doesn't work. It writes :
0
Error Details:
java.lang.ArrayIndexOutOfBoundsException: 0
at edu.caltech.sbw.analyses.TimeBasedAnalysisApplication.main(TimeBasedAnalysisApplication.java:75)
context:
java.lang.Exception
at edu.caltech.sbw.SBWException.appendStackTrace(SBWException.java:300)
at edu.caltech.sbw.SBWException.<init>(SBWException.java:289)
at edu.caltech.sbw.SBWRawException.<init>(SBWRawException.java:100)
at edu.caltech.sbw.SBWException.translateException(SBWException.java:334)
at edu.caltech.sbw.analyses.TimeBasedAnalysisApplication.main(TimeBasedAnalysisApplication.java:143)
-----------
But it doesn't matter. I can successfully use, for example, JarnacLite.exe or SimDriverNET.exe instead.
The problem is that I need a simulator that can understand SBML and where I could add some new functionality. I am reluctant to write everything by myself. So it is very appealing to use your Jar's..
Best regards,
Valentina
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I'm sorry for the trouble, it would seem that we have been talking about different applications. There are actually two Java Versions of the SimDriver available. The one being SimDriver.java, which is a legacy version that we have not used in ages. There also is a SimDriverJava.jar which will allow you to perform simple time course simulations, perhaps this would be worth a look.
best
Frank
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Hello,
I would like to use SimDriver.jar. Do you you have some documentation for it?
Thanks in advance,
Valentina
Hello Valentina,
the SimDriver jar file, is a very small front end that will enable you to perform timecourse simulations with various simulators. We wrote the application to provide access to the simulators for users that don't have access the the C# version of the program which is more powerful. But back to the Java version:
- to start it a simple double click on the Jar file should suffice.
Once the Application starts, a click on "Load Model" will enable you to load any sbml file. After that you specify the start and endpoint, as well as the number of output points you would like to see. Finally a click on simulate will simulate the model and plot the results.
Please let me know whether this worked for you.
thank you
best
Frank
Hello Frank,
Just double clicking on SimDriver.jar doesn't work. It writes :
0
Error Details:
java.lang.ArrayIndexOutOfBoundsException: 0
at edu.caltech.sbw.analyses.TimeBasedAnalysisApplication.main(TimeBasedAnalysisApplication.java:75)
context:
java.lang.Exception
at edu.caltech.sbw.SBWException.appendStackTrace(SBWException.java:300)
at edu.caltech.sbw.SBWException.<init>(SBWException.java:289)
at edu.caltech.sbw.SBWRawException.<init>(SBWRawException.java:100)
at edu.caltech.sbw.SBWException.translateException(SBWException.java:334)
at edu.caltech.sbw.analyses.TimeBasedAnalysisApplication.main(TimeBasedAnalysisApplication.java:143)
-----------
But it doesn't matter. I can successfully use, for example, JarnacLite.exe or SimDriverNET.exe instead.
The problem is that I need a simulator that can understand SBML and where I could add some new functionality. I am reluctant to write everything by myself. So it is very appealing to use your Jar's..
Best regards,
Valentina
I'm sorry for the trouble, it would seem that we have been talking about different applications. There are actually two Java Versions of the SimDriver available. The one being SimDriver.java, which is a legacy version that we have not used in ages. There also is a SimDriverJava.jar which will allow you to perform simple time course simulations, perhaps this would be worth a look.
best
Frank