A computer-implemented method for simulating a cell culture process, comprising: receiving one or more measurable parameter values relating to one or more operating conditions of the cell culture process, the one or more operating conditions including one or more of: fresh media feed flow rate, fresh media composition, cell bleed flow rate, harvest flow rate, temperature, pH, dissolved oxygen, agitation rate; simulating the cell culture process using: a model of the cell culture process; estimated values of unmeasurable parameters in the model; and the received one or more measurable parameter values; receiving information indicating desired cell growth in the cell culture process; and determining, according to a result of said simulating the cell culture process, optimal operating conditions for obtaining the desired cell growth, wherein the model of the cell culture process describes the cell culture process with coupled ordinary differential equations including measurable parameters and the unmeasurable parameters, one or more of the measurable parameters relating to said one or more operating conditions of the cell culture process; wherein one or more of the unmeasurable parameters relate to lysed cells in the cell culture process; wherein said one or more of the unmeasurable parameters include concentration of the lysed cells in the cell culture process and/or concentration of a biomaterial that has a toxic influence on the viable cells, the concentration of the lysed cells being tracked through modeling disintegration of dead cells, production of a toxic biomaterial being modeled as a function of viable cell density, wherein the modeling of the disintegration of the dead cells involves cell death rate that is adjusted by the concentration of the lysed cells and/or concentration of the toxic biomaterial; and wherein the estimated values of the unmeasurable parameters are estimated using Bayesian inference with measurable parameter values that are measured with respect to at least one operation of the cell culture process. receiving one or more measurable parameter values relating to one or more operating conditions of the cell culture process, the one or more operating conditions including one or more of: fresh media feed flow rate, fresh media composition, cell bleed flow rate, harvest flow rate, temperature, pH, dissolved oxygen, agitation rate; simulating the cell culture process using: a model of the cell culture process; estimated values of unmeasurable parameters in the model; and the received one or more measurable parameter values; a model of the cell culture process; estimated values of unmeasurable parameters in the model; and the received one or more measurable parameter values; receiving information indicating desired cell growth in the cell culture process; and determining, according to a result of said simulating the cell culture process, optimal operating conditions for obtaining the desired cell growth, wherein the model of the cell culture process describes the cell culture process with coupled ordinary differential equations including measurable parameters and the unmeasurable parameters, one or more of the measurable parameters relating to said one or more operating conditions of the cell culture process; wherein one or more of the unmeasurable parameters relate to lysed cells in the cell culture process; wherein said one or more of the unmeasurable parameters include concentration of the lysed cells in the cell culture process and/or concentration of a biomaterial that has a toxic influence on the viable cells, the concentration of the lysed cells being tracked through modeling disintegration of dead cells, production of a toxic biomaterial being modeled as a function of viable cell density, wherein the modeling of the disintegration of the dead cells involves cell death rate that is adjusted by the concentration of the lysed cells and/or concentration of the toxic biomaterial; and wherein the estimated values of the unmeasurable parameters are estimated using Bayesian inference with measurable parameter values that are measured with respect to at least one operation of the cell culture process.