EcoSimNet: a Framework for Ecological Simulations

The simulation of physical, chemical and biological processes in coastal ecosystems is used as a way to understand the system internal dynamics and to predict its evolution over time, in order to promote behaviours environmentally friendly and to induce effective and efficient management of the ecosystem as a whole. The complexity and diversity of those processes encompass wide areas of knowledge, involving many researchers and research teams for their mathematical modelling. Each research team adopts a given programming language to translate the model to a computer application, simulating the processes that they are specialists and are interested in, rarely thinking about the possibility of its integration with other models developed by other research teams, that simulate complementary processes. These applications are normally self-contained and, when used in a management context, require a lot of extra work to export and import results from one application to another, in order to share the knowledge acquired and complement the simulation. Furthermore, they do not integrate any kind of human rationality embedded to help a decision making activity. The work presented in this document explores the capacity for the realistic simulation of complex systems, working consistently, integrating results generated by processes simulated in distinct applications and placing the human reasoning in the middle of the decision making system. It presents a framework for modelling and simulating coastal ecosystems and an associated methodology for creating an Environmental Decision Support Systems (EDSS). Both are based on object oriented programming (OOP) and, in the case of the EDSS, on Autonomous Intelligent Agents. The modelling software simulator (EcoDynamo) is written in C++ and includes several object dynamic link libraries (DLLs) for the simulation of the different physical and biogeochemical processes. These libraries were designed to be linked with different model shells, possibly written in different programming languages, for the sake of portability and reusability. A high level communication language (ECOLANG) was developed to allow the communications between EcoDynamo and the agents and applications that belong to the system. ECOLANG was designed to describe ecological systems in terms of regional characteristics, living agent’s perceptions and actions and is independent from any hardware or software platform. The framework (Ecological Simulation Network – EcoSimNet) was developed to easily integrate and bring together the several pieces of the system – the simulator is the core of the framework and all the agents/applications communicate with it; the agents have, also, the ability to communicate with each other and can define several scenarios for the simulation in order to optimize their own objectives. To improve the speed of the simulation process, the infrastructure provides mechanisms to integrate several simulators, enabling the parallel simulation of different configuration scenarios to increase the simulation speed. The EDSS uses the Analytic Hierarchy Process methodology (AHP) to integrate multiple qualitative and quantitative conflicting criteria. The user gives a structure with a pairwise comparison between criteria based on its importance, and a priority ranking of the pre-processed scenarios is achieved. To validate the portability of the DLLs, some objects were integrated in the COHERENS simulator (written in Fortran), and some processes simulated by COHERENS were invoked by the EcoDynamo simulator. To validate the EcoSimNet framework, the simulation system was used both to simulate the Sungo Bay model (People’s Republic of China) and Ria Formosa (Algarve, Portugal). The simulation system was used to simulate several distinct ecosystem configurations in order to demonstrate its flexibility. The framework was also used to optimize different scenarios with bivalve farming areas, and the EDSS was used with different management scenarios in the Ria Formosa lagoon (Portugal). The experiments performed indicate that these tools may be widely used by people involved in the management of coastal areas to integrate environmental, economic and social issues in the decision process, without an in-depth knowledge of modelling methodologies.

Agent-based modeling in biology allows, firstly, to simulate a multi-component environment with a number of entities (plants, microbes, fungi, insects, birds, mammals etc.) and, secondly, to perform numerical experiments for different research purposes. The article presents modeling software for natural and rural ecosystems based on the food chain concept. This software encompasses C++ core and Jupyter/Python data analysis environment; it supports both an interactive and a batch run modes; it allows exporting data for further processing and visualizes the data analysis results. Agent features and motion strategies can be defined with the program interface. The software allows modeling ecosystem dynamics with respect to inter-and cross-species relations through the simulation of agent analytical models in ecosystem world. We applied a three-species test model "plant-herbivore-carnivore" (PHC model) to perform software code validation. As a testing scenario, foraging impact to the overall PHC model balance was evaluated during the series of software try-outs.

19th European Conference …, 2005

Our paper deals with the information system Info-X. This software system aims at the management of ecological studies and provides a special functionality for simulation studies. In particular, Info-X can be seen as an approach to conserve the wealth of knowledge and experience, which manifests in models, simulation programs, and their practical applications. This knowledge/experience can broadly support research in theoretical and practical ecology. Info-X provides a state-of-the-art graphical user-interface to browse its database, select desired content, start simulation runs with suitable simulators, and check published results for plausibility/correctness. Furthermore, users can assess and rate the quality of existing content and are invited to submit new content.

Advances in computational intelligence and robotics book series, 2017

The objective of this paper is to reflect on our experience in a serious game research project, named SimParc, about multi-agent support for participatory management of protected areas for biodiversity conservation and social inclusion. Our project has a clear filiation with the MAS-RPG methodology developed by the ComMod action-research community, where multi-agent simulation (MAS) computes the dynamics of the resources and role-playing game (RPG) represents the actions and dialogue between stakeholders about the resources. We have explored some specific directions, such as: dialogue support for negotiation; argumentation-based decision making and its explanation; technical assistance to the players based on viability modeling. In our project, multi-agent based simulation focuses on the negotiation process itself, performed by human players and some artificial participants/agents, rather than on the simulation of the resources dynamics. Meanwhile, we have also reintroduced the modeling of the socioecosystem dynamics, but as a local technical assistance/analysis tool for the players.

There is a growing demand for " end-to-end " models, which are modeling tools used to analyze and understand the fundamental complexities of marine ecosystems and processes emerging from the interaction of individuals from different trophic groups with respect to the physical environment and, even, human activity. These models are valuable quantitative tools for ecosystem-based management. To explore potential answers to complex questions regarding ecosystems using these models, it is necessary to incorporate classical ontogenic changes through the life cycle of target individuals, in addition to inherited behavioral strategies, as an additional differentiating aspect, particularly when the behavior has a direct impact on the ecosystem phenomena under study. However, it is difficult to combine different fine scale time and spatial granularities to infer animal behavior and ontogenic development. This complexity has kept these two levels of analysis separated, because most current tools do not have the required computational resources and advanced software architecture. To address this issue, we propose an individual-based modeling framework that is capable of handling and unifying the two experimental categories with a comprehensive biological and behavioral model that strictly adheres to the physiological functions of ingestion, growth, and metabolism of organisms. In addition, this model incorporates the exchange and transfer of mass and energy through local interactions at all trophic levels (lower to higher), the physical environment, and anthropogenic activity. For the framework to model short time events, such as classical predator–prey interactions , while also generating long-term ecosystem emergent properties, a special interleaving scheduling engine and physical space computer model was devised, which optimizes memory and processing resources. The framework was tested through several experiments with a three-population ecosystem containing up to 40 thousand organisms evolving inside a 200,000 m 2 simulation environment during 12,000 model-hours; yet, requiring only a few hours of program execution on a regular personal computer. The model included various environmental physical elements, such as several hundred shelters, the number of which can be easily modified in each experiment to simulate substrate degradation and its impact on populations. With the aid of the quantitative and qualitative tools provided by the model, it was possible to observe a coupling between prey and predator population dynamics. In conclusion, we confirmed that the end-to-end model developed here could successfully generate detailed specific hypotheses about fish behavior and quantify impacts on population dynamics.