MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments

Research and Education in Computational Science and Engineering

Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie

Embodied Robot Models for Interdisciplinary Emotion Research

Due to their complex nature, emotions cannot be properly understood from the perspective of a single discipline. In this paper, I discuss how the use of robots as models is beneficial for interdisciplinary emotion research. Addressing this issue through the lens of my own research, I focus on a critical analysis of embodied robots models of different aspects of emotion, relate them to theories in psychology and neuroscience, and provide representative examples. I discuss concrete ways in which embodied robot models can be used to carry out interdisciplinary emotion research, assessing their contributions: as hypothetical models, and as operational models of specific emotional phenomena, of general emotion principles, and of specific emotion ``dimensions''. I conclude by discussing the advantages of using embodied robot models over other models.Peer reviewe

The Mechanics of Embodiment: A Dialogue on Embodiment and Computational Modeling

Embodied theories are increasingly challenging traditional views of cognition by arguing that conceptual representations that constitute our knowledge are grounded in sensory and motor experiences, and processed at this sensorimotor level, rather than being represented and processed abstractly in an amodal conceptual system. Given the established empirical foundation, and the relatively underspecified theories to date, many researchers are extremely interested in embodied cognition but are clamouring for more mechanistic implementations. What is needed at this stage is a push toward explicit computational models that implement sensory-motor grounding as intrinsic to cognitive processes. In this article, six authors from varying backgrounds and approaches address issues concerning the construction of embodied computational models, and illustrate what they view as the critical current and next steps toward mechanistic theories of embodiment. The first part has the form of a dialogue between two fictional characters: Ernest, the �experimenter�, and Mary, the �computational modeller�. The dialogue consists of an interactive sequence of questions, requests for clarification, challenges, and (tentative) answers, and touches the most important aspects of grounded theories that should inform computational modeling and, conversely, the impact that computational modeling could have on embodied theories. The second part of the article discusses the most important open challenges for embodied computational modelling

Modelling dynamic decision making with the ACT-R cognitive architecture

This paper describes a model of dynamic decision making in the Dynamic Stocks and Flows (DSF) task, developed using the ACT-R cognitive architecture. This task is a simple simulation of a water tank in which the water level must be kept constant whilst the inflow and outflow changes at varying rates. The basic functions of the model are based around three steps. Firstly, the model predicts the water level in the next cycle by adding the current water level to the predicted net inflow of water. Secondly, based on this projection, the net outflow of the water is adjusted to bring the water level back to the target. Thirdly, the predicted net inflow of water is adjusted to improve its accuracy in the future. If the prediction has overestimated net inflow then it is reduced, if it has underestimated net inflow it is increased. The model was entered into a model comparison competition-the Dynamic Stocks and Flows Challenge-to model human performance on four conditions of the DSF task and then subject the model to testing on five unseen transfer conditions. The model reproduced the main features of the development data reasonably well but did not reproduce human performance well under the transfer conditions. This suggests that the principles underlying human performance across the different conditions differ considerably despite their apparent similarity. Further lessons for the future development of our model and model comparison challenges are considered