Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices

Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems, a diverse array of biological systems have been the target of large-scale computational modeling efforts. Nonetheless, these research agendas have yet to prove decisively their value among the broader community of theoretical and experimental biologists. In this commentary, we examine a range of philosophical and practical issues relevant to understanding the potential of integrative simulations. We discuss the role of theory and modeling in different areas of physics and suggest that certain sub-disciplines of physics provide useful cultural analogies for imagining the future role of simulations in biological research. We examine philosophical issues related to modeling which consistently arise in discussions about integrative simulations and suggest a pragmatic viewpoint that balances a belief in philosophy with the recognition of the relative infancy of our state of philosophical understanding. Finally, we discuss community workflow and publication practices to allow research to be readily discoverable and amenable to incorporation into simulations. We argue that there are aligned incentives in widespread adoption of practices which will both advance the needs of integrative simulation efforts as well as other contemporary trends in the biological sciences, ranging from open science and data sharing to improving reproducibility.Comment: 10 page

Impersonal efficiency and the dangers of a fully automated securities exchange

This report identifies impersonal efficiency as a driver of market automation during the past four decades, and speculates about the future problems it might pose. The ideology of impersonal efficiency is rooted in a mistrust of financial intermediaries such as floor brokers and specialists. Impersonal efficiency has guided the development of market automation towards transparency and impersonality, at the expense of human trading floors. The result has been an erosion of the informal norms and human judgment that characterize less anonymous markets. We call impersonal efficiency an ideology because we do not think that impersonal markets are always superior to markets built on social ties. This report traces the historical origins of this ideology, considers the problems it has already created in the recent Flash Crash of 2010, and asks what potential risks it might pose in the future

Federated Robust Embedded Systems: Concepts and Challenges

The development within the area of embedded systems (ESs) is moving rapidly, not least due to falling costs of computation and communication equipment. It is believed that increased communication opportunities will lead to the future ESs no longer being parts of isolated products, but rather parts of larger communities or federations of ESs, within which information is exchanged for the benefit of all participants. This vision is asserted by a number of interrelated research topics, such as the internet of things, cyber-physical systems, systems of systems, and multi-agent systems. In this work, the focus is primarily on ESs, with their specific real-time and safety requirements. While the vision of interconnected ESs is quite promising, it also brings great challenges to the development of future systems in an efficient, safe, and reliable way. In this work, a pre-study has been carried out in order to gain a better understanding about common concepts and challenges that naturally arise in federations of ESs. The work was organized around a series of workshops, with contributions from both academic participants and industrial partners with a strong experience in ES development. During the workshops, a portfolio of possible ES federation scenarios was collected, and a number of application examples were discussed more thoroughly on different abstraction levels, starting from screening the nature of interactions on the federation level and proceeding down to the implementation details within each ES. These discussions led to a better understanding of what can be expected in the future federated ESs. In this report, the discussed applications are summarized, together with their characteristics, challenges, and necessary solution elements, providing a ground for the future research within the area of communicating ESs

Virtual Reality Games for Motor Rehabilitation

This paper presents a fuzzy logic based method to track user satisfaction without the need for devices to monitor users physiological conditions. User satisfaction is the key to any product’s acceptance; computer applications and video games provide a unique opportunity to provide a tailored environment for each user to better suit their needs. We have implemented a non-adaptive fuzzy logic model of emotion, based on the emotional component of the Fuzzy Logic Adaptive Model of Emotion (FLAME) proposed by El-Nasr, to estimate player emotion in UnrealTournament 2004. In this paper we describe the implementation of this system and present the results of one of several play tests. Our research contradicts the current literature that suggests physiological measurements are needed. We show that it is possible to use a software only method to estimate user emotion

Developments in Practice V: IT Sourcing: Build, Buy, or Market

This paper describes the logical evolution of IT service provisioning through various delivery models over time concentrating on the rent era as well as the market era - an emerging external IT services marketplace that offers rich opportunities for IT organizations to become more cost-effective in the future. With the market era, IT organizations speculate that strategic business applications for mission-critical applications will remain in-house but delivery for standard and meta-industry applications, processes, and technology will be off-site. Thus, for most companies, it is likely that external IT providers will form part of their future service delivery package and that some IT departments will become both consumers and sellers of components. The implications of these developments for IT management are articulated and the elements of an IT sourcing strategy presented

Scientific Research about Climate Change Mitigation in Transport : A critical review

Peer reviewedPostprin

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

Spartan Daily, May 13, 2004

Volume 122, Issue 67https://scholarworks.sjsu.edu/spartandaily/10001/thumbnail.jp

Life of occam-Pi

This paper considers some questions prompted by a brief review of the history of computing. Why is programming so hard? Why is concurrency considered an “advanced” subject? What’s the matter with Objects? Where did all the Maths go? In searching for answers, the paper looks at some concerns over fundamental ideas within object orientation (as represented by modern programming languages), before focussing on the concurrency model of communicating processes and its particular expression in the occam family of languages. In that focus, it looks at the history of occam, its underlying philosophy (Ockham’s Razor), its semantic foundation on Hoare’s CSP, its principles of process oriented design and its development over almost three decades into occam-? (which blends in the concurrency dynamics of Milner’s ?-calculus). Also presented will be an urgent need for rationalisation – occam-? is an experiment that has demonstrated significant results, but now needs time to be spent on careful review and implementing the conclusions of that review. Finally, the future is considered. In particular, is there a future