'make sim' builds a linux/jack emulated version of each module. bfin_sim is a work in progress. In particular, the more complex modules don't work quite right in the emulator, possibly due to small numerical discrepancies between emulation & hardware.
Emulator is a super-valuable tool, but at this stage be prepared to potentially report and/or fix emulator bugs. My aleph dev branch has some brand new bugfixes compared to monome dev branch. I used it to develop 'hard' features like biquad filters, polyblep antialiasing, cubic-spline interpolation & adsr envelopes offline using linux. Actually these kinds of problems are not so tough when you smash on them with such mighty hammers as printf, gnuplot, gdb & jaaa:
it covers nearly half the functionality of aleph. There are 2 separate cpu chips in the aleph - one for control, one for DSP. This emulator attempts to cover the DSP part (aka blackfin or bfin). BEES has a linux build target called beekeep, which can be used in a more limited way to develop new BEES features. It doesn't currently communicate with the bfin emulator...
You can ping the DSP params using osc, but the whole thing may not make a load of sense without getting to know BEES a little bit with an aleph (this runs on the controller cpu aka avr32). Also some of the special instructions are still missing from the emulator. I'm only just now getting into the fract16 primitives, which are being added on ad-hoc as required e.g: this commit.