At the moment, when I copy the .jar file to CytoscapeConfiguration/3/apps/installed, Cytoscape crashes and gives the following error:
Native code library failed to load.
java.lang.UnsatisfiedLinkError: no CopasiJava in java.library.path: [/home/people/hkaya/Cytoscape_v3.8.2/framework/lib, /home/people/hkaya/Cytoscape_v3.8.2/framework/lib, /usr/java/packages/lib, /usr/lib64, /lib64, /lib, /usr/lib]
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How does this work in COPASI's java bindings?
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Thank you for the detailed explanation. By that logic, I can get an expression for the flux by model.getReaction(index).getFluxReference().getCN.toString(); correct?
I just didn't quite understand the following:but I would suggest that you manually create a plot for the elements you want to use, open it in a text editor, and look at the `ChannelSpec` element to see how they should look like.
Do you mean I should save the plot as a txt file to find the ChannelSpec?
Write a separate class that reads this expression, separates it into its components
gets the common name for each object in the expression according to the string. (e.g., if it is Flux.something, get the fluxValueReference, if it is [something], get the common name for the concentration, and so on)
After converting them into their CN format, it surrounds each object with < > brackets.
It then feeds this revised formula back into the Optimization task.
Do you think this is doable, or is it way more complex than it should've been?