We use python for pretty much everything in my research group -- high-level scripting of simulations written in C; controlling experiments over serial, GPIB, us

We use python for pretty much everything in my research group -- high-level scripting of simulations written in C; controlling experiments over serial, GPIB, usb; and data analysis and plotting for publications. I used Matlab for several years prior, but got really annoyed by the limits of the language when you try to do anything beyond matrix manipulation. Python + scipy + pylab is a pretty effective replacement for matlab prototyping and data analysis, with a much better general purpose language and FFI. Anything that needs to be fast you can write in C/C++ and wrap with swig or ctypes so that you can still use a high-level language to run all your simulations, and do the data analysis as well.