The signature left in quasar spectra by neutral hydrogen in the Universe allows constraining the sum of the neutrino masses with a better sensitivity than laboratory experiments and may shed new light on the neutrino mass hierarchy and the absolute mass-scale of neutrinos . Constraints on cosmological parameters and on the dark energy equation of state can also be derived from a joint parameter estimation procedure . However , this requires a detailed modeling of the line-of-sight power spectrum of the transmitted flux in the Lyman- \alpha ( Ly \alpha ) forest on scales ranging from a few to hundreds of megaparsecs , which in turn demands the inclusion and careful treatment of cosmological neutrinos . To this end , we present here a suite of state-of-the-art hydrodynamical simulations with cold dark matter ( CDM ) , baryons and massive neutrinos , specifically targeted for modeling the low-density regions of the intergalactic medium ( IGM ) as probed by the Ly \alpha forest at high-redshift . The simulations span volumes ranging from ( 25 ~ { } h ^ { -1 } { Mpc } ) ^ { 3 } to ( 100 ~ { } h ^ { -1 } { Mpc } ) ^ { 3 } , and were made using either 3 \times 192 ^ { 3 } \simeq 21 million or 3 \times 768 ^ { 3 } \simeq 1.4 billion particles . The resolution of the various runs was further enhanced , so that we reached the equivalent of 3 \times 3072 ^ { 3 } \simeq 87 billion particles in a ( 100 ~ { } h ^ { -1 } { Mpc } ) ^ { 3 } box size . The chosen cosmological parameters are compatible with the latest Planck ( 2013 ) results , although we also explored the effect of slight variations in the main cosmological and astrophysical parameters . We adopted a particle-type implementation of massive neutrinos , and consider three degenerate species with masses \sum m _ { \nu } = 0.1 , 0.2 , 0.3 , 0.4 , and 0.8 eV , respectively . We improved on previous studies in several ways , in particular with updated routines for IGM radiative cooling and heating processes , and initial conditions based on second-order Lagrangian perturbation theory ( 2LPT ) rather than the Zel ’ dovich approximation . This allowed us to safely start our runs at relatively low redshift ( z = 30 ) , which reduced the shot-noise contamination in the neutrino component and the CPU consumption . In addition to providing technical details on the simulations , we present the first analysis of the nonlinear three- and one-dimensional matter and flux power spectra from these models , and characterize the statistics of the transmitted flux in the Ly \alpha forest including the effect of massive neutrinos . In synergy with recent data from the Baryon Acoustic Spectroscopic Survey ( BOSS ) and the Planck satellite , and with a grid of corresponding neutrino-less simulations , our realizations will allow us to constrain cosmological parameters and neutrino masses directly from the Ly \alpha forest with improved sensitivity . In addition , our simulations can be useful for a broader variety of cosmological and astrophysical applications , ranging from the three-dimensional modeling of the Ly \alpha forest to cross-correlations between different probes , studying the expansion history of the Universe including massive neutrinos , and particle-physics related topics . Moreover , while our simulations have been specifically designed to meet the requirements of the BOSS survey , they can also be used for upcoming or future experiments – such as eBOSS and DESI .