In recent years, the interest in high intensity proton beams in excess of several milli-amperes has risen. Potential applications are in neutrino physics, materials and energy research, and isotope production. Continuous wave proton beams of five to ten milli-amperes are now in reach due to advances in accelerator technology and through improved understanding of the beam dynamics. As an example application, we present the proposed IsoDAR experiment, a search for so-called sterile neutrinos and non-standard interaction using the KamLAND detector located in Japan. We present updated sensitivities for this experiment and describe in detail the design of the high intensity proton driver that uses several novel ideas. These are: accelerating H2+ instead of protons, directly injecting beam into the cyclotron via a radio frequency quadrupole, and carefully matching the beam to achieve so-called vortex motion. The preliminary design holds up well in PIC simulation studies and the injector system is now being constructed, to be commissioned with a 1MeV/amu test cyclotron.