Modelling plasma-based seeded soft X-ray lasers from the creation of the plasma to the propagation of a femtosecond high-order harmonic (HOH) seed throughout several millimetres of inhomogeneous plasma is a complex challenge. Different spatio-temporal scales from the hydrodynamic evolution of the plasma (hundreds of micrometres and nanoseconds) to the propagation of pulses through the plasma (millimetres and tens of picoseconds), electron collisions (picoseconds or even shorter) and the evolution of the envelope of the seeded HOH (tens of femtoseconds) must be tackled in order to fully understand these systems. In this paper, we will present the multi-scale computational paradigm that we have used to perform a full ab initio simulation of a dense, Ni-like Krypton plasma amplifier of soft X-rays. Results of the modelling and expected future applications will also be shown.