The product is configured by sending particular midi System Exclusive (SysEx) messages to its midi out. All the software does is let you enter the value for some setting, and then the software stuffs the value into the needed SysEx message sent to the Brain's midi out.
Since the Brain is USB-Midi compliant, ALSA will detect its midi in and out ports.
All you need is a linux app that lets you enter/send a Sysex message. There are a number of those, starting with the simple command line pmidi.
And of course you need a list of the Brain's Sysex messages. Here they are:http://wiki.lividinstruments.com/wiki/Brain_Jr_Sysex
In fact, this configuration software is so simplistic, I could throw together a gui app that sets those parameters you need to adjust. Bottom line: Don't worry about the config software running on linux.