How to create a database from Java using FB embedded?
You don't need to use isql, gbak or any external too. There is a class provided by Jaybird called org.firebirdsql.management.FBManager.
Here's an example how to use it:
FBManager manager = new FBManager("EMBEDDED");
manager.createDatabase("/path/to/database_file.fdb", 'usr', 'pwd');
First parameter is the database filename, and second and third parameters are username and password. Since username and are not checked by Firebird (at least on Windows version of embedded), you can provide any two strings.