With the ever-increasing flow of high-throughput gene expression, protein interaction and genome sequence data, researchers gradually approach a system-level understanding of cells and even multi-cellular organisms. Systems biology is an emerging field that enables us to achieve in-depth understanding at the system level. For this, we need to establish methodologies and techniques that enable us to understand biological systems as systems, which means to understand: (1) the structure of the system, such as gene/metabolic/signal transduction networks and physical structures, (2) the dynamics of such systems, (3) methods to control systems, and (4) methods to design and modify systems to generate desired properties. However, the meaning of "system-level understanding" is still ambiguous. This paper reviews the current status of the field and outlines future research directions and issues that need to be addressed.