The overall goal of the ESIGNET project is to study the computational properties of cell signalling networks (CSN) by evolving them using methods from evolutionary computation, and to re-apply this understanding in developing new ways to model and predict real CSNs.

Finding an appropriate framework to specify the desired computational properties of CSNs is essential for all subsequent parts of the ESIGNET project. This includes identification of objectives with regard to the target solution which is represented as a formal description of CSNs. In this report, we summarise different criteria important for CSN representation, simulation, evaluation, and optimisation. These criteria as a whole form a framework oriented to an effective and efficient analysis in silico. We distinguish between criteria containing descriptive, structural, dynamical, and functional properties. Beyond these criteria, we introduce different levels for formal representation of target functions able to specify CSN behaviour from a computational point of view. In addition to this, selected techniques useful for CSN specification and evaluation are presented.