Data to model pipeline. The data world (public and private pathway databases/interactomes and -omics data sets supplementing existing models and kinetics data) is used to inform the model building process via several processes: building of a prior knowledge network, of a data-derived (inferred) network, and their refinement and training to data (color coding and terminology are described in ). Red ovals represent components of the CellNOptR toolkit and orange ovals represent other representative computational tools outside the logic model formalism. Simulation of models generated from existing data sets can be performed via different methods, not limited to ordinary differential equation or logic models. Data not used initially (such as spatial features, information about molecular domains, or wider parameter range), and the new simulation results can be used iteratively to refine model building process. Potential connections between different modeling and simulation approaches (currently only possible via ad-hoc implementations) are shown as dashed lines.