Astrophysical neutrinos measured by ICECUBE challenge existing models of multi-messenger sources. Goal of thesis is modeling of sources of cosmic rays, gamma rays and neutrinos taking into account all experimental constraints from direct measurements, KASCADE-Grande and Pierre Auger Observatory for cosmic rays, HESS, Fermi and CTA for gamma-rays and ICECUBE/km3 for neutrinos, study propagation of cosmic rays and gamma-rays in the Galaxy and intergalactic space, search for the imprints of such sources in the experimental data.