To be able to rapidly implement and adapt high level software applications to the Free Electron Laser in Hamburg (FLASH), we developed a flexible API using the DOOCS DAQ system*. The continuous extensions and improvements of the FLASH facility, requires not only fast development of tightly integrated control loops, but also robust and well calibrated software to be used in the daily user operation. The middle layer of the DAQ system is a perfect place for attaching such applications since all machine data is here available in a synchronized form. The API has been designed to not only allow attaching native C++ programs but also the widely used MATLAB software applications. The general functionality of this API and the work flow to implement these software applications will be shown in an example of the advanced energy measurement application and the rapid development of a simple PID controller.