Agents in Bioinformatics

The scope of the Technical Forum Group (TFG) on Agents in Bioinformatics (BIOAGENTS) was to inspire collaboration between the agent and bioinformatics communities with the aim of creating an opportunity to propose a different (agent-based) approach to the development of computational frameworks both for data analysis in bioinformatics and for system modelling in computational biology. During the day, the participants examined the future of research on agents in bioinformatics primarily through 12 invited talks selected to cover the most relevant topics. From the discussions, it became clear that there are many perspectives to the field, ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages for use by information agents, and to the use of Grid agents, each of which requires further exploration. The interactions between participants encouraged the development of applications that describe a way of creating agent-based simulation models of biological systems, starting from an hypothesis and inferring new knowledge (or relations) by mining and analysing the huge amount of public biological data. In this report we summarise and reflect on the presentations and discussions

A survey of simulation techniques in commerce and defence

Despite the developments in Modelling and Simulation (M&S) tools and techniques over the past years, there has been a gap in the M&S research and practice in healthcare on developing a toolkit to assist the modellers and simulation practitioners with selecting an appropriate set of techniques. This study is a preliminary step towards this goal. This paper presents some results from a systematic literature survey on applications of M&S in the commerce and defence domains that could inspire some improvements in the healthcare. Interim results show that in the commercial sector Discrete-Event Simulation (DES) has been the most widely used technique with System Dynamics (SD) in second place. However in the defence sector, SD has gained relatively more attention. SD has been found quite useful for qualitative and soft factors analysis. From both the surveys it becomes clear that there is a growing trend towards using hybrid M&S approaches

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

Simulation of complex environments:the Fuzzy Cognitive Agent

The world is becoming increasingly competitive by the action of liberalised national and global markets. In parallel these markets have become increasingly complex making it difficult for participants to optimise their trading actions. In response, many differing computer simulation techniques have been investigated to develop either a deeper understanding of these evolving markets or to create effective system support tools. In this paper we report our efforts to develop a novel simulation platform using fuzzy cognitive agents (FCA). Our approach encapsulates fuzzy cognitive maps (FCM) generated on the Matlab Simulink platform within commercially available agent software. We firstly present our implementation of Matlab Simulink FCMs and then show how such FCMs can be integrated within a conceptual FCA architecture. Finally we report on our efforts to realise an FCA by the integration of a Matlab Simulink based FCM with the Jack Intelligent Agent Toolkit

Multi-level agent-based modeling - A literature survey

During last decade, multi-level agent-based modeling has received significant and dramatically increasing interest. In this article we present a comprehensive and structured review of literature on the subject. We present the main theoretical contributions and application domains of this concept, with an emphasis on social, flow, biological and biomedical models.Comment: v2. Ref 102 added. v3-4 Many refs and text added v5-6 bibliographic statistics updated. v7 Change of the name of the paper to reflect what it became, many refs and text added, bibliographic statistics update