Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

From Social Simulation to Integrative System Design

As the recent financial crisis showed, today there is a strong need to gain "ecological perspective" of all relevant interactions in socio-economic-techno-environmental systems. For this, we suggested to set-up a network of Centers for integrative systems design, which shall be able to run all potentially relevant scenarios, identify causality chains, explore feedback and cascading effects for a number of model variants, and determine the reliability of their implications (given the validity of the underlying models). They will be able to detect possible negative side effect of policy decisions, before they occur. The Centers belonging to this network of Integrative Systems Design Centers would be focused on a particular field, but they would be part of an attempt to eventually cover all relevant areas of society and economy and integrate them within a "Living Earth Simulator". The results of all research activities of such Centers would be turned into informative input for political Decision Arenas. For example, Crisis Observatories (for financial instabilities, shortages of resources, environmental change, conflict, spreading of diseases, etc.) would be connected with such Decision Arenas for the purpose of visualization, in order to make complex interdependencies understandable to scientists, decision-makers, and the general public.Comment: 34 pages, Visioneer White Paper, see http://www.visioneer.ethz.c

Agent-Based Models and Simulations in Economics and Social Sciences: from conceptual exploration to distinct ways of experimenting

Now that complex Agent-Based Models and computer simulations spread over economics and social sciences - as in most sciences of complex systems -, epistemological puzzles (re)emerge. We introduce new epistemological tools so as to show to what precise extent each author is right when he focuses on some empirical, instrumental or conceptual significance of his model or simulation. By distinguishing between models and simulations, between types of models, between types of computer simulations and between types of empiricity, section 2 gives conceptual tools to explain the rationale of the diverse epistemological positions presented in section 1. Finally, we claim that a careful attention to the real multiplicity of denotational powers of symbols at stake and then to the implicit routes of references operated by models and computer simulations is necessary to determine, in each case, the proper epistemic status and credibility of a given model and/or simulation

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: NL

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: N

Overview of crowd simulation in computer graphics

High-powered technology use computer graphics in education, entertainment, games, simulation, and virtual heritage applications has led it to become an important area of research. In simulation, according to Tecchia et al. (2002), it is important to create an interactive, complex, and realistic virtual world so that the user can have an immersive experience during navigation through the world. As the size and complexity of the environments in the virtual world increased, it becomes more necessary to populate them with peoples, and this is the reason why rendering the crowd in real-time is very crucial. Generally, crowd simulation consists of three important areas. They are realism of behavioral (Thompson and Marchant 1995), high-quality visualization (Dobbyn et al. 2005) and convergence of both areas. Realism of behavioral is mainly used for simple 2D visualizations because most of the attentions are concentrated on simulating the behaviors of the group. High quality visualization is regularly used for movie productions and computer games. It gives intention on producing more convincing visual rather than realism of behaviors. The convergences of both areas are mainly used for application like training systems. In order to make the training system more effective, the element of valid replication of the behaviors and high-quality visualization is added

Potential applications of simulation modelling techniques in healthcare: lessons learned from aerospace and military

The Aerospace and Military areas are to do with complex missions and situations. Modelling and Simulation (M&S) has been applied in many areas of defence ranging from space sciences, satellite engineering to multi-warfare (air warfare, undersea warfare), air & missile defence, acquisition, tactical military trainings & exercises, national security analysis and strategic decision making & planning, etc. The application of simulation modelling techniques in healthcare would improve the provision of healthcare services; however, their application has been much relatively feeble in the healthcare sector as compared to the defence sector. This paper presents results from a systematic literature survey on applications of modelling simulation techniques in the Aerospace & Military. The knowledge gained or lessons learned from the survey were finally used to analyze the potential applications of the simulation modelling techniques to the healthcare sector. Results show that in the defence sector, Distributed Simulation has now become a widely adopted technique. However, System Dynamics (SD) and Discrete Event Simulation (DSE) have also gained relative attention. From this survey it becomes clear that various simulation modelling techniques are useful for specific purposes and have potential applications in the healthcare sector

Complex Systems Science: Dreams of Universality, Reality of Interdisciplinarity

Using a large database (~ 215 000 records) of relevant articles, we empirically study the "complex systems" field and its claims to find universal principles applying to systems in general. The study of references shared by the papers allows us to obtain a global point of view on the structure of this highly interdisciplinary field. We show that its overall coherence does not arise from a universal theory but instead from computational techniques and fruitful adaptations of the idea of self-organization to specific systems. We also find that communication between different disciplines goes through specific "trading zones", ie sub-communities that create an interface around specific tools (a DNA microchip) or concepts (a network).Comment: Journal of the American Society for Information Science and Technology (2012) 10.1002/asi.2264

Agent-Based Models and Simulations in Economics and Social Sciences

Now that complex Agent-Based Models and computer simulations spread over economics and social sciences - as in most sciences of complex systems -, epistemological puzzles (re)emerge. We introduce new epistemological concepts so as to show to what extent authors are right when they focus on some empirical, instrumental or conceptual significance of their model or simulation. By distinguishing between models and simulations, between types of models, between types of computer simulations and between types of empiricity obtained through a simulation, section 2 gives the possibility to understand more precisely - and then to justify - the diversity of the epistemological positions presented in section 1. Our final claim is that careful attention to the multiplicity of the denotational powers of symbols at stake in complex models and computer simulations is necessary to determine, in each case, their proper epistemic status and credibility.Agent-Based Models and Simulations ; Epistemology ; Economics ; Social Sciences ; Conceptual Exploration ; Model World ; Credible World ; Experiment ; Denotational Hierarchy

Overview on agent-based social modelling and the use of formal languages

Transdisciplinary Models and Applications investigates a variety of programming languages used in validating and verifying models in order to assist in their eventual implementation. This book will explore different methods of evaluating and formalizing simulation models, enabling computer and industrial engineers, mathematicians, and students working with computer simulations to thoroughly understand the progression from simulation to product, improving the overall effectiveness of modeling systems.Postprint (author's final draft