Several simulation tools allow studying the impact of agricultural management on production activities in specific environments. Such tools are specialized, to different extents, to specific production activities: arable crops/cropping systems, grassland, orchards, agroforestry, livestock etc. Also, their focus includes to various degrees the estimate of system externalities which may have a negative environmental impact. Furthermore, the structure of such tools does neither allow an easy plug-in of modules for different agricultural production activities, nor the use of different approaches for the simulation of processes via alternate components. Finally, such systems are proprietary systems of either research groups or projects. The SEAMLESS project aims at providing a tool to integrate analyses of impacts on a wide range of aspects of sustainability and multi-functionality of agriculture. This requires evaluating agricultural production and system externalities for most, if not all, types of agricultural production systems. It also requires the availability of a simulation framework which can be extended and updated by research teams with possibly different expertise, which allows a manageable transfer of research results to operational tools, and which is transparent with respect to its contents and its functionality. The Agricultural Production and Externalities Simulator is a modular simulation system targeted at estimating the biophysical behaviour of agricultural production systems in response to the interaction of soil-weather and different options of agro-technical management. APES is currently meant to be used at field scale, simulating 1-D fluxes (future version will also use 2-D fluxes to account for multiple cropping). All modules of this release are first prototypes linked to test the hypothesis on the component based structure and to evaluate consequent modelling and technical issues; outputs should not be analyzed to evaluate model performance at this stage. APES is an application which uses several components being developed to offer simulation options for different processes of relevance in agricultural production systems. Models are described in the associated help files of components, and a shared ontology is being built on specifically to a given modelling framework, are also meant to be a concrete option to share modelling knowledge with other projects and the scientific community. This report presents a description of the current state of development of APES (release 0.3; June 2006).