A Cytoscape app to connect to a Neo4j database and execute extensions of the Neo4j database. This app has been extended to query the shortest path for metabolic conversions.

Minimum System Requirements (for CyNeo4j 2.x):

• Neo4j 3.5.x (requires Java 8 but can run with Java 11 as well)
• Cytoscape 3.9.x (automatically comes with a Java 11 download)
• Java 11 (Eclipse)

Compiling the script The setup of this project in Eclipse has been tested with:

• Eclipse IDE 2022-06 (Java and Web developers), OS Linux (Ubuntu 18.04.6 LTS), JRE JavaSE-11.

Find the app in the Cytoscape app store (http://apps.cytoscape.org/apps/cyneo4j) and on Github (https://github.com/cyneo4j/cyNeo4j).

For a tutorial and installation guide for the server side component checkout https://cyneo4j.github.io/DSMN/ !

Build this project from the command line:

mvn clean install

Update the app through Eclipse:

1. (Fork and) clone this repository; open Eclipse and create a new workspace.
2. Import this project by clicking "Import projects..." in the package explorer, select Git > Projects from Git > Existing local repository.
3. Add the folder where you cloned this repository, click Finish, Next, and Finish.
4. Build this repository with the Maven dependancies using the pom.xml file; rightclick on file, select "Maven > Update Project"
5. Create a launch configuration using the pom.xml file; rightclick on file, select "Run as > Run configurations...". Provide a name, and add as goal 'clean install'. Click Apply, click 'Run'
6. Build the jar with existing launch configuration using the pom.xml file; rightclick on file, select "Run as > Maven Build".

Icons from: http://openclipart.org/detail/7983/red-+-green-ok-not-ok-icons-by-tzeeniewheenie