Use of Kinetikit and GENESIS for modeling signaling pathways.

Computer modeling is a way of doing experiments in silico , to bridge the gap between precise theories of simplified systems and the complexity of experimental biology. Modeling harnesses computer power to scale theoretical calculations Lip from equations describing individual reactions, to more lifelike systems involving thousands of interacting molecules. The start and end point of this process is experiment: from data to predictions to further data. The ideal of the modeling process is to gain insights into system function along the way. Modeling has tended to be the preserve of the mathematician or computer scientist, but its greatest value is in the hands of the experimentalist. Modern simulation systems seek to reach their users in two ways: first, by providing a simple graphical interface suitable for nonprogrammers, and second, by tying closely into advances in web-based databases to tap into better data. This chapter is based on the "well-stirred" approach, with compartmentalization as a slight elaboration.