The field of system biology focuses on creating a finely detailed picture of biological mechanisms. Recently, the need has arisen for more and more sophisticated and mathematically well founded computational tools capable of analyzing the models that are and will be at the core of system biology. Such computational models should be implemented in software packages faithfully while exploiting the potential trade-offs among usability, accuracy, and scalability dealing with large amounts of data. The aim of this talk is that of introducing some emerging problems and proposed solutions in this context.