This document is both a synthesis of current notions about complex systems and a practical approach description. A disambiguation is proposed and exposes possible reasons for controversies related to causation and emergence. Theoretical considerations about simulations are presented. A justification is then given for the development of practical tools and techniques for the investigation of complex systems. A methodology for the usage of these tools is finally suggested, illustrated by application examples. © 2008 Wiley Periodicals, Inc. Complexity, 2009.