Not able to squeeze the rate equation in cell designer using SBML squeezer as a plugin

[angithamelvin]

I am currently using the SBML squeezer plugin for squeezing the rate equations for the network drawn using cell designer 4.4.2 for my project work. I downloaded the SBML squeezer plugin.(www.cogsys.cs.unituebingen.de/software/SBMLsqueezer/downloads/jsbml-1. 1-a1-incl-libs.jar)
While using the software plugin I encountered the following issues;

1. I am being able to get only individual rate equations for the network drawn using the cell designer but when I apply the SBML squeezer for the whole network I get no equations in the list
2. I tried exporting the equations by clicking the tab "export changes" but no file is being created
3. I am also unable to simulate the network because the rate equations are not getting added to the reactions in the network
4. The model report is not generated and is showing a java.io.IOException error. (I have installed java version 8 update before all installations)
   SBMLsqueezer.docx

[draeger]

Dear @angithamelvin, was there a specific reason for not downloading the most recent JAR file from this GitHub page directly? The link you provided does not work and also seems to refer to JSBML rather than SBMLsqueezer.

My suggestion to you would be to try out what happens if you export your model from CellDesigner and store it in SBML format. Then, you could use the most recent version of SBMLsqueezer and run it outside of CellDesigner. Please note that SBMLsqueezer is also usable as a stand-alone tool.

Also, regarding the export, it seems like there is a problem with access rights in your target folder. Could you please check your file permissions where you want to store the report?

[angithamelvin]

Thank you Sir for your email I will try this Regards Angitha Melvin

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On Thu, 15 Sep 2022 at 9:32 PM, Andreas Dräger ***@***.***> wrote: Dear @angithamelvin <https://github.com/angithamelvin>, was there a specific reason for not downloading the most recent JAR file from this GitHub <https://github.com/draeger-lab/SBMLsqueezer/releases> page directly? The link you provided does not work and also seems to refer to JSBML rather than SBMLsqueezer. My suggestion to you would be to try out what happens if you export your model from CellDesigner and store it in SBML format. Then, you could use the most recent version of SBMLsqueezer <https://github.com/draeger-lab/SBMLsqueezer/releases/download/v2.2/SBMLsqueezer-2.2.jar> and run it outside of CellDesigner. Please note that SBMLsqueezer is also usable as a stand-alone tool. Also, regarding the export, it seems like there is a problem with access rights in your target folder. Could you please check your file permissions where you want to store the report? — Reply to this email directly, view it on GitHub <#17 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A3CVU6YHHENU6M6AOT2P57DV6NCBVANCNFSM6AAAAAAQNI56CI> . You are receiving this because you were mentioned.Message ID: ***@***.***>