Carbon mitigation has become a prior concern for industry, since the global policies progressively head to an imposition on greenhouse gases emissions reduction. Thenceforth, technology is developing in the sake of offering technical and economic answers, able to implement an autonomous business. Biotechnology offers a multilevel added-value and readiness carbon based outlets. Nevertheless, state of art shows numerous engineering, energetic integration and economic assessment constrains limiting deployability. The aim of this work is to present the progress on multi-program platforms applied to the conversion of CO2 contained in exhaust gases from incinerators and its conversion into bio-materials. SYCTOM facilities of Saint-Ouen and Issy-les-Moulineaux, France, are the reference facilities. This work proposes a systemic understanding of photobioreactors and down-stream processes by a multi-physics and multi-system process. Modelling work towards process optimization consists on building a computer super-structure as follows: - C++ and VBA codes pilots data exchange between programs, - Aspen Tech (Plus and HYSYS) are considered for down-stream process simulation (unitary operations), - COMSOL and in house Matlab/Modelica perform the modelling CO2 mass transfer from flue gases to the liquid phase with cyanobacteria, growth with complex kinetics that include water saturation level, multi-phase flow control, light penetration, and chemicals availability, - Matlab, COMSOL and other CFD tools enable novel technologies of biomass harvesting to be coded and considered in the full process, - Matlab and Modelica tools include optimization routines based on genetic algorithms to improve the performance of the full CO2 to bio-material processes. This work highlighted the potential application of combining different modelling programs and opened new perspectives for further highly complex processes and system requiring such engineering development.