SHOGUN comes as a stand-a-lone program accepting input via command-line or from a script file, where standard file IO is used to read in /write out data (optionally even tcp/ip). More importantly, it interfaces to established matrix and statistics packages, such as Matlab(tm), Octave, R and Python. SHOGUN comes in three flavours, the so called Modular Interfaces, the Static Interfaces, and the Eierlegendewollmilchsau Interface

The modular interfaces are very flexible in nature, as they allow an arbitrary number of objects potentially interacting together. For example several SVMs with using multiple kernels or preprocessors, with the kernels relying on other machine learning methods (like e.g. HMMs). The modular interfaces are automatically generated by a tool called SWIG, and some languages are better supported than others. Currently the best supported and most extensively tested modular interface is for Python, but the Octave, Java, Ruby, C#, R and Lua interfaces are also supported though not as extensively tested. For further information see Modular Interfaces

The static interfaces are cross language compatible, i.e. the syntax for calling shogun from python,R,matlab,octave is the same (with minor exceptions). However only a singly object of each type is supported (e.g. only a single SVM classifier). In case you are dealing with more complex models it is suggested to use the object oriented, very flexible python-modular interface. Note that all interfaces should work equally well, though some may not support more advanced data types like byte matrices. For further information see Static Interfaces

The special Eierlegende Wollmilchsau (elwms) interface is a chimera that in one file interfaces to python,R,matlab,octave. Using it provides one with the advantage of running e.g., python or R scripts within octave (where variables are passed in memory). see ELWMS Interface