Kepler is described as 'free open-source software system for designing, executing, reusing, evolving, archiving, and sharing scientific workflows' and is an app in the Education & Reference category. There are five alternatives to Kepler for Mac, Windows, Linux, Online / Web-based and Chrome OS. The best alternative is Xcos, which is both free and Open Source. Other great apps like Kepler are OpenModelica (Free, Open Source), Simulink (Paid), Scicos (Free, Open Source) and StochSD (Free, Open Source).
Scicos is a graphical dynamical system modeler and simulator developed in the Metalau project at INRIA, Paris-Rocquencourt center. With Scicos, user can create block diagrams to model and simulate the dynamics of hybrid dynamical systems and compile models into executable code.
StochSD (Stochastic System Dynamics) is a System Dynamics simulation software with focus on stochastics. It is a form of Continuous System Simulation (CSS) that in addition to model and simulate continuous flows between compartments, can handle transitions of discrete entities.