Several software tools are available that facilitate the use of the NONMEM software and extend its functionality. This tutorial shows how three commonly used and freely available tools, Pirana, PsN, and Xpose, form a tightly integrated workbench for modeling and simulation with NONMEM. During the tutorial, we provide some guidance on what diagnostics we consider most useful in pharmacokinetic model development and how to construct them using these tools.CPT: Pharmacometrics & Systems Pharmacology (2013) 2, e50; doi:10.1038/psp.2013.24; advance online publication 26 June 2013.