The goal of this project is to develope a plugin for the the plugin-framework insilico. Said plugin should offer the user the full functionality of the drawing tool krayon4sbgn embedded in insilico, for example displaying editing files of the .sbgn format. At a later point the plugin should also be enabled to interact with other plugins which can be used to display and execute sbml files. At the final state this plugin can be used as an important component of a configuration of insilico optimized for work in systems biology.
In the first two months of working time several problems with setting up insilico and and krayon4sbgn had to be fixed. Some of them like compiling krayon4sgbn using the eclipse IDE and building insilico using Maven under windows still haven't been fixed. A meeting with Roland Wiese brought up the current approach that is editing krayon4sbgn using IntelliJ and developing the plugin importing classes from the krayon4sbgn.jar file in the build path. A modified version of the krayon4sbgn project that can be used as a resource for this project can be found here. Even though the beginning of coding was delayed by unforeseen problems there had already been learn-effects regarding setting up the java and kotlin compiler and build path and working with eclipse and IntelliJ as well as working with software with commercial licence and obfuscation. Shortly after that a working JavaFX Appliction making most features of krayon4insilico available was finished. This state of work is located on the master branch. Up to this point Drag and Drop which is central for krayon4sbgn functionality does not work inside a javaFX swingNode. It was decided to keep this issue open and continue working on plugin development. In the following weeks problems with insilicos maven build occured leading to a bug fix for insilicos maven build under Windows. In the last weeks of working time the current state of the project with the final plugin structures consisting of a bundle the corresponding feature and osgi-services were finished. The plugin still contains several bugs. For this see Issues and next steps.
Start by installing insilico so it can be started in eclipse. replace git files and README.md with the corresponding files from this project and add the krayon4insilico bundle und feature to insilicos bundles and features. The easiest way to do this is to copy the content of your insilico project to this project.
Supervisor: Dr. Andreas Draeger