I am currently doing my Ph.D. in Computational Science at the University of Cape Town. My project is about developing systems biology tools for the modelling, simulation, and analysis of glycosylation networks found in Muc-1 type breast cancer tumours.
Unlike many system biology tools on Cytoscape, I want to approach the network from an enzyme kinetics angle because glycosylation networks involve a lot of glycosyltransferases that determine the final structure of glycan chains.
Long story short, I found the java language bindings for COPASI, and decompiled the .class files into the .java files.
Then, I created a maven project in cytoscape-api using eclipse, and copied these java files here.
I know that I need to write a proper CyActivator.java file, but have no idea where to start. The language bindings for COPASI are way too many and a bit complicated. What would be a simple first-step to see that it can at least be installed successfully and start without failing?
I created a .jar file after updating the pom.xml file (find attached), but 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]
Any guidance would be greatly appreciated!
All the best,