Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics.

Background: Given the complex mechanisms underlying biochemical processes systems biology researchers tend to build ever increasing computational models. However, dealing with complex systems entails a variety of problems, e.g.

Accessible methods for the dynamic time-scale decomposition of biochemical systems.

Motivation: The growing complexity of biochemical models asks for means to rationally dissect the networks into meaningful and rather independent subnetworks. Such foregoing should ensure an understanding of the system without any heuristics employed. Important for the success of such an approach is its accessibility and the clarity of the presentation of the results.

COPASI--a COmplex PAthway SImulator.

Motivation: Simulation and modeling is becoming a standard approach to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods.

Results: Here, we present COPASI, a platform-independent and user-friendly biochemical simulator that offers several unique features.