Agent Street: An Environment for Exploring Agent-Based Models in Second Life

Urban models can be seen on a continuum between iconic and symbolic. Generally speaking, iconic models are physical versions of the real world at some scaled down representation, while symbolic models represent the system in terms of the way they function replacing the physical or material system by some logical and/or mathematical formulae. Traditionally iconic and symbolic models were distinct classes of model but due to the rise of digital computing the distinction between the two is becoming blurred, with symbolic models being embedded into iconic models. However, such models tend to be single user. This paper demonstrates how 3D symbolic models in the form of agent-based simulations can be embedded into iconic models using the multi-user virtual world of Second Life. Furthermore, the paper demonstrates Second Life\'s potential for social science simulation. To demonstrate this, we first introduce Second Life and provide two exemplar models; Conway\'s Game of Life, and Schelling\'s Segregation Model which highlight how symbolic models can be viewed in an iconic environment. We then present a simple pedestrian evacuation model which merges the iconic and symbolic together and extends the model to directly incorporate avatars and agents in the same environment illustrating how \'real\' participants can influence simulation outcomes. Such examples demonstrate the potential for creating highly visual, immersive, interactive agent-based models for social scientists in multi-user real time virtual worlds. The paper concludes with some final comments on problems with representing models in current virtual worlds and future avenues of research.Agent-Based Modelling, Pedestrian Evacuation, Segregation, Virtual Worlds, Second Life

DynaMoVis: Visualization of dynamic models for urban modeling

In association with Urban modelers, we have created DynaMoVis, a system for the visualization of dynamic models. The prediction of the evolution of urban and ecological systems is difficult because they are complex nonlinear systems that exhibit self-organization, emergence and path dependence. Without a good understanding of the dynamics, interventions might have unintended side-effects. This study aims to make progress in the understanding of dynamic models in the application areas of urban modelling. Analyzing these simulations is challenging due to the large amount of data generated and the high-dimensional nature of the system. We present a visualization system for exploring the behavior of a simulation from many different points of view. The system contains a number of different modes which allow exploration of: the simulation parameter space, the introduction and effect of noise on the simulation and the basins of attraction in the phase space of the simulation. Through use of this system it has been possible to develop a deeper understanding of the inter-dependencies in the models, their parameter spaces and corresponding phase spaces

Order of Magnitude Markers: An Empirical Study on Large Magnitude Number Detection

In this paper we introduce Order of Magnitude Markers (OOMMs) as a new technique for number representation. The motivation for this work is that many data sets require the depiction and comparison of numbers that have varying orders of magnitude. Existing techniques for representation use bar charts, plots and colour on linear or logarithmic scales. These all suffer from related problems. There is a limit to the dynamic range available for plotting numbers, and so the required dynamic range of the plot can exceed that of the depiction method. When that occurs, resolving, comparing and relating values across the display becomes problematical or even impossible for the user. With this in mind, we present an empirical study in which we compare logarithmic, linear, scale-stack bars and our new markers for 11 different stimuli grouped into 4 different tasks across all 8 marker types

Speed/Accuracy Trade-Off between the Habitual and the Goal-Directed Processes

Instrumental responses are hypothesized to be of two kinds: habitual and goal-directed, mediated by the sensorimotor and the associative cortico-basal ganglia circuits, respectively. The existence of the two heterogeneous associative learning mechanisms can be hypothesized to arise from the comparative advantages that they have at different stages of learning. In this paper, we assume that the goal-directed system is behaviourally flexible, but slow in choice selection. The habitual system, in contrast, is fast in responding, but inflexible in adapting its behavioural strategy to new conditions. Based on these assumptions and using the computational theory of reinforcement learning, we propose a normative model for arbitration between the two processes that makes an approximately optimal balance between search-time and accuracy in decision making. Behaviourally, the model can explain experimental evidence on behavioural sensitivity to outcome at the early stages of learning, but insensitivity at the later stages. It also explains that when two choices with equal incentive values are available concurrently, the behaviour remains outcome-sensitive, even after extensive training. Moreover, the model can explain choice reaction time variations during the course of learning, as well as the experimental observation that as the number of choices increases, the reaction time also increases. Neurobiologically, by assuming that phasic and tonic activities of midbrain dopamine neurons carry the reward prediction error and the average reward signals used by the model, respectively, the model predicts that whereas phasic dopamine indirectly affects behaviour through reinforcing stimulus-response associations, tonic dopamine can directly affect behaviour through manipulating the competition between the habitual and the goal-directed systems and thus, affect reaction time

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead