Models come in many forms. We all use conceptual models on a daily basis. Driving to the store, we know when to turn right or left, because we have in our minds a mental picture of the street scenes. Even if we do not know a city well, we have learned how to read and interpret a street map, which in itself is a model of the city. Dolls and toy trains are physical models that allow children to learn much about the world of adults. A good architect sees from a blueprint what a building will look like. In addition to conceptual models, which always whirr about in a scientist's mind, systems biology makes heavy use of mathematical and computational models. The difference between the two is actually quite vague, as many mathematical models are analyzed with computers and computational models are based on mathematical formulae and equations.

A typical model in systems biology consists of a mathematical description of processes occurring in cells, organisms, populations or ecosystems. To see why such models can be helpful, consider, as an analogy, the computer system in an airplane as it prepares for landing. It takes input information from the real world, such as the speed and weight of the plane, power of the jets, current altitude, length of the runway, as well as environmental conditions like wind speed and direction, enters all these data into a large system of mathematical equations, evaluates these equations, and determines the appropriate settings of rudders, flaps, and slats that ensure a smooth landing. The concepts in biology are similar, and one might imagine inputs regarding the health status of a diseased person, which are computationally converted into suggestions for a treatment. The modeling process itself is more complicated than for engineered systems because we often do not know the biological component parts and processes sufficiently well. It also turns out that knowledge of the parts is not sufficient to reconstruct a biological system, as we will discuss later.

In his 1858 book, The Autocrat of the Breakfast Table, the American physician, writer and poet Oliver Wendell Holmes mused, “I find that the great thing in this world is not so much where we stand as in what direction we are moving.”