The IOPT-Flow modeling framework is a Web-based set of tools for the design of embedded and cyber-physical system controllers, comprehending a graphical editor, a simulator and automatic code generation tools. Models are designed using an hybrid formalism combining Petri nets and data-flows to specify the reactive and data-driven parts of the controllers. Model composition based on components simplify the development of complex systems, that may be assembled with the help of a library of previously designed components. The synergy of the interaction between data-flow and Petri net elements brings many advantages to the design of mixed systems that must simultaneously perform data processing operations on input signals and manage complex event driven state-machines. The resulting controllers may be implemented on software or reconfigurable hardware devices, as the code generation tools support C and VHDL. The tools are free to use and are available online http://gres.uninova.pt/iopt-flow.