Systems biology model databases and resources.

Systems biology aims at a quantitative understanding of systemic behaviour as a function of its components and their interactions. In systems biology studies computer models play an important role: (i) to integrate the components' behaviour and (ii) to analyse experimental data sets. With the growing number of kinetic models that are being constructed for parts of biological systems, it has become important to store these models and make them available in a standard form, such that these models can be combined, eventually leading to a model of a complete system. In the present chapter we describe database initiatives that contain kinetic models for biological systems, together with a number of other systems biology resources related to kinetic modelling.

Data and model integration using JWS Online.

Systems Biology requires a tight integration of experimental data and detailed computer models to obtain a quantitative understanding of the system under study. To facilitate this integration a standardization of data and model representation and storage is important. We illustrate here such an integration using JWS Online, the modeling tool developed in our group. We follow the approach of the Silicon Cell project for the construction and validation of kinetic models and discuss some issues with respect to storage of experimental data and models. The majority of the published kinetic models for biological systems have been developed for metabolic networks and this will be our focus in this manuscript. It is not our aim to present here an all encompassing method for data and model integration, but rather to present our work on this topic to start a discussion in which the different initiatives, methods and tools can be compared.