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DNA replication is one of the most fundamental processes in the life of every cell. In earlier work a model to capture the mechanics of the DNA replication process was developed. The model allowed us to make novel predictions regarding the mechanisms behind DNA replication based on experimental data for the fission yeast. One of the difficulties we had to overcome in the process was tuning of the model parameters based on experimental data, which, for lack of better methods had to be done manually. Here we propose a methodology for systematizing this process, inspired by techniques for multi-objective optimization.