FRASystem: fault tolerant system using agents in distributed computing systems

In this paper, we present a fault tolerant and recovery system called FRASystem (Fault Tolerant & Recovery Agent System) using multi-agent in distributed computing systems. Previous rollback-recovery protocols were dependent on an inherent communication and an underlying operating system, which caused a decline of computing performance. We propose a rollback-recovery protocol that works independently on an operating system and leads to an increasing portability and extensibility. We define four types of agents: (1) a recovery agent performs a rollback-recovery protocol after a failure, (2) an information agent constructs domain knowledge as a rule of fault tolerance and information during a failure-free operation, (3) a facilitator agent controls the communication between agents, (4) a garbage collection agent performs garbage collection of the useless fault tolerance information. Since agent failures may lead to inconsistent states of a system and a domino effect, we propose an agent recovery algorithm. A garbage collection protocol addresses the performance degradation caused by the increment of saved fault tolerance information in a stable storage. We implemented a prototype of FRASystem using Java and CORBA and experimented the proposed rollback-recovery protocol. The simulations results indicate that the performance of our protocol is better than previous rollback-recovery protocols which use independent checkpointing and pessimistic message logging without using agents. Our contributions are as follows: (1) this is the first rollback-recovery protocol using agents, (2) FRASystem is not dependent on an operating system, and (3) FRASystem provides a portability and extensibility.     

Design and analysis of a replicated server architecture for supporting IP–host mobility

Mobility support in IP networks requires servers to forward packets to mobile hosts and to maintain information pertaining to a mobile host's location in the network. In the mobile Internet Protocol (mobile-IP), location and packet forwarding functions are provided by servers referred to as home agents. These home agents may become the bottleneck when there are a large number of mobile hosts in the network. In this paper, we consider the design and analysis of a replicated server architecture in which multiple home agents are used to provide mobility support. In order to minimize the delay across the home agents, one of the key aspects is the design of load balancing schemes in which a home agent may transfer the control of a mobile host to another home agent in the same network. The methods for triggering the transfer and the policy for selecting the next home agent define various load balancing schemes which have different performance characteristics. In this paper, we design a protocol that forms the building block for implementing such load balancing schemes, and we then study the performance characteristics of three selection schemes, namely, random, round-robin, and join the shortest queue (JSQ), and three transfers policies, namely, timer-, counter- and threshold-based. The key results of this study are as follows: (1) The results show that both random and round-robin selection policies can yield modest load balancing gains, and that these gains increase when the traffic is more bursty (burstiness is defined as the ratio of the peak arrival rate to the mean arrival rate) as well as when there are more home agents. (2) The threshold-based transfer policy performs better than timer-based and counter-based policies, since in threshold-based policies transfers are made only when the queue is overloaded, unlike counter- and timer-based policies in which transfers can be made from an unloaded home agent to an overloaded home agent. This revised version was published online in August 2006 with corrections to the Cover Date.     

Microfluidics for cryopreservation

Cryopreservation has utility in clinical and scientific research but implementation is highly complex and includes labor-intensive cell-specific protocols for the addition/removal of cryoprotective agents and freeze-thaw cycles. Microfluidic platforms can revolutionize cryopreservation by providing new tools to manipulate and screen cells at micro/nano scales, which are presently difficult or impossible with conventional bulk approaches. This review describes applications of microfluidic tools in cell manipulation, cryoprotective agent exposure, programmed freezing/thawing, vitrification, and in situ assessment in cryopreservation, and discusses achievements and challenges, providing perspectives for future development.     

A Supervisory Control Approach for Execution Control of an FMC

This paper presents a generic methodology based on formal language theory for the modeling and control of flexible manufacturing cell (FMC) systems. The motivating idea behind the overall approach stems from the supervisory control theory under the framework of Ramadge and Wonham. Essentially, we characterize the asynchronous and dynamic behavior of an FMC as a regular language and formulate the control logic generation problem as a sublanguage calculation problem, which requires the resulting language to satisfy at least two properties: maximal permissiveness and controllability. Then an algorithm for resolving the problem is presented. Based on the solution of the problem called supervisor, we propose a controller architecture that guarantees coordinated operation of an FMC through the regulation of occurrences of events. An adaptive control policy that regenerates supervisors on changes in task configurations is presented and a dynamic equation that describes the evolution of the control logic along time is derived. Then, we show that the proposed maximally permissive adaptive control policy has a number of preferred properties, including computational efficiency and consistency between the successive supervisors. Finally, a controller for an example FMC is implemented, using the object-oriented software modules. Our procedure has the merit of mathematical soundness, modular design, and systematic implementation.     

Analysis of interaction for mixtures of agents using the linear isobole

The linear isobole that is commonly used as a reference for the study of interaction is derived from the interaction of an agent with itself. It is shown that the general use of the linear isobole in the study of the combined effects of mixtures of agents implies interaction between the agents whether the dose-effect curves of the agents are the same or not. It is difficult to generalize the interaction between two doses of the same agent to the interaction between two doses of different agents with different action mechanisms without the use of a mechanistic model. Predictions using non-interaction defined as independent action are generally different from those using linear isobole. A simple mechanistic framework based on the concept of common intermediate lesions is introduced in this paper to relate these two methods used for the analysis of synergism and antagonism. In this framework of lesion development, two agents that have no common intermediate lesion in their action will be non-interactive (referred to as independent action). When the two agents share a common intermediate, it is shown that the combined effect will follow the linear isobole (referred to as common action). This simple framework of analysis is applicable to the general study of interaction between two agents with different types of dose-effect curves.     

How to reach linguistic consensus: a proof of convergence for the naming game

In this paper we introduce a mathematical model of naming games. Naming games have been widely used within research on the origins and evolution of language. Despite the many interesting empirical results these studies have produced, most of this research lacks a formal elucidating theory. In this paper we show how a population of agents can reach linguistic consensus, i.e. learn to use one common language to communicate with one another. Our approach differs from existing formal work in two important ways: one, we relax the too strong assumption that an agent samples infinitely often during each time interval. This assumption is usually made to guarantee convergence of an empirical learning process to a deterministic dynamical system. Two, we provide a proof that under these new realistic conditions, our model converges to a common language for the entire population of agents. Finally the model is experimentally validated.     

A Mathematical Framework for Modeling Axon Guidance

In this paper, a simulation tool for modeling axon guidance is presented. A mathematical framework in which a wide range of models can been implemented has been developed together with efficient numerical algorithms. In our framework, models can be defined that consist of concentration fields of guidance molecules in combination with finite-dimensional state vectors. These vectors can characterize migrating growth cones, target neurons that release guidance molecules, or other cells that act as sources of membrane-bound or diffusible guidance molecules. The underlying mathematical framework is presented as well as the numerical methods to solve them. The potential applications of our simulation tool are illustrated with a number of examples, including a model of topographic mapping.     

Plant-mediated interactions: Considerations for agent selection in weed biological control programs

Plant-mediated indirect interactions among herbivores (arthropods and pathogens) are common and extensively reported in the ecological literature. However, they are not well-documented with respect to weed biological control. Such interactions between biological control agents can have net positive or negative impacts on total weed suppression depending on the strength of the interaction(s), the relative importance of the agent indirectly impacted, and the combined weed suppression that results. A better understanding of plant-mediated interactions may improve decision-making about which agents to introduce in classical biological control programs for greatest impact on invasive weeds. This paper reviews the subject, including examples from the biological control literature; outlines the need for research on indirect effects of herbivores on other herbivores; discusses how such knowledge may strengthen classical biological control programs for invasive weeds; and provides recommendations for the kind of studies that should be done and how information about plant-mediated interactions could be integrated into agent evaluation protocols, to assist in decision-making about agents for importation and release.     

Language Lateralization in Children Aged 10 to 11 Years: A Combined fMRI and Dichotic Listening Study

Objective

The aims of this study were to develop and assess a method to map language networks in children with two auditory fMRI protocols in combination with a dichotic listening task (DL). The method is intended for pediatric patients prior to epilepsy surgery. To evaluate the potential clinical usefulness of the method we first wanted to assess data from a group of healthy children.

Methods

In a first step language test materials were developed, intended for subsequent implementation in fMRI protocols. An evaluation of this material was done in 30 children with typical development, 10 from the 1^st, 4^th and the 7^th grade, respectively. The language test material was then adapted and implemented in two fMRI protocols intended to target frontal and posterior language networks. In a second step language lateralization was assessed in 17 typical 10–11 year olds with fMRI and DL. To reach a conclusion about language lateralization, firstly, quantitative analyses of the index data from the two fMRI tasks and the index data from the DL task were done separately. In a second step a set of criteria were applied to these results to reach a conclusion about language lateralization. The steps of these analyses are described in detail.

Results

The behavioral assessment of the language test material showed that it was well suited for typical children. The results of the language lateralization assessments, based on fMRI data and DL data, showed that for 15 of the 17 subjects (88%) a conclusion could be reached about hemispheric language dominance. In 2 cases (12%) DL provided critical data.

Conclusions

The employment of DL combined with language mapping using fMRI for assessing hemispheric language dominance is novel and it was deemed valuable since it provided additional information compared to the results gained from each method individually.     

Local information-based control for probabilistic swarm distribution guidance

This paper proposes a closed-loop decentralised framework for swarm distribution guidance, which disperses homogeneous agents over bins to achieve a desired density distribution by using feedback gains from the current swarm status. The key difference from existing works is that the proposed framework utilises only local information, not global information, to generate the feedback gains for stochastic policies. Dependency on local information entails various advantages including reduced inter-agent communication, a shorter timescale for obtaining new information, asynchronous implementation, and deployability without a priori mission knowledge. Our theoretical analysis shows that, even utilising only local information, the proposed framework guarantees convergence of the agents to the desired status, while maintaining the advantages of existing closed-loop approaches. Also, the analysis explicitly provides the design requirements to achieve all the advantages of the proposed framework. We provide implementation examples and report the results of empirical tests. The test results confirm the effectiveness of the proposed framework and also validate the robustness enhancement in a scenario of partial disconnection of the communication network.     

Implementation of biosurety systems in a Department of Defense medical research laboratory

New biosurety regulations and guidelines were implemented in 2003 because of increased concern for the safety and security of biological select agents and toxins (BSAT) that may be used as weapons of mass destruction. Biosurety is defined as the combination of security, biosafety, agent accountability, and personnel reliability needed to prevent unauthorized access to select agents of bioterrorism. These new regulations will lead to increased scrutiny of the use of select biological agents in registered research laboratories, but the regulations may have unintended effects on cost, progress, and perceptions in programs previously considered part of the academic research community. We review the history of biosurety, evolving guidelines, implementation of the regulations, and impacts at the lead research laboratory for medical biological defense for the Department of Defense.     

Viola: A New Visual Programming Language Designed for the Rapid Development of Interacting Agent Systems

The construction of complex simulation models and the application of new computer hardware to ecological problems has resulted in the need for many ecologists to rely on computer programmers to develop their modelling software. However, this can lead to a lack of flexibility and understanding in model implementation and in resource problems for researchers. This paper presents a new programming language, Viola, based on a simple organisational concept which can be used by most researchers to develop complex simulations much more easily than could be achieved with standard programming languages such as C++. The language is object oriented and implemented through a visual interface. It is specifically designed to cope with complicated individual based behavioural simulations and comes with embedded concurrency handling abilities.     

Decentralized self-selection of swarm trajectories: from dynamical systems theory to robotic implementation

In this paper, we present a distributed control strategy, enabling agents to converge onto and travel along a consensually selected curve among a class of closed planar curves. Individual agents identify the number of neighbors within a finite circular sensing range and obtain information from their neighbors through local communication. The information is then processed to update the control parameters and force the swarm to converge onto and circulate along the aforementioned planar curve. The proposed mathematical framework is based on stochastic differential equations driven by white Gaussian noise (diffusion processes). Using this framework, there is maximum probability that the swarm dynamics will be driven toward the consensual closed planar curve. In the simplest configuration where a circular consensual curve is obtained, we are able to derive an analytical expression that relates the radius of the circular formation to the agent’s interaction range. Such an intimate relation is also illustrated numerically for more general curves. The agent-based control strategy is then translated into a distributed Braitenberg-inspired one. The proposed robotic control strategy is then validated by numerical simulations and by implementation on an actual robotic swarm. It can be used in applications that involve large numbers of locally interacting agents, such as traffic control, deployment of communication networks in hostile environments, or environmental monitoring.     

Piezoelectrically Actuated Biomimetic Self-Contained Quadruped Bounding Robot

This paper presents the development of a mesoscale self-contained quadruped mobile robot that employs two pieces ofpiezocomposite actuators for the bounding locomotion.The design of the robot leg is inspired by legged insects and animals,and the biomimetic concept is implemented in the robot in a simplified form,such that each leg of the robot has only one degreeof freedom.The lack of degree of freedom is compensated by a slope of the robot frame relative to the horizontal plane.For theimplementation of the self-contained mobile robot,a small power supply circuit is designed and installed on the robot.Experimentalresults show that the robot can locomote at about 50 mm·s^-1with the circuit on board,which can be considered as asignificant step toward the goal of building an autonomous legged robot actuated by piezoelectric actuators.     

European Electronic Personal Health Records initiatives and vulnerable migrants: A need for greater ethical,legal and social safeguards

The effective collection and management of personal data of rapidly migrating populations is important for ensuring adequate healthcare and monitoring of a displaced peoples’ health status. With developments in ICT data sharing capabilities, electronic personal health records (ePHRs) are increasingly replacing less transportable paper records. ePHRs offer further advantages of improving accuracy and completeness of information and seem tailored for rapidly displaced and mobile populations. Various emerging initiatives in Europe are seeking to develop migrant‐centric ePHR responses. This paper highlights their importance and benefits, but also identifies a number of significant ethical, legal and social issues (ELSI) and challenges to their design and implementation, regarding (1) the kind of information that should be stored, (2) who should have access to information, and (3) potential misuse of information. These challenges need to be urgently addressed to make possible the beneficial use of ePHRs for vulnerable migrants in Europe.     

A Framework for Assessment of Ecological Risks from Multiple Activities

The standard framework for ecological risk assessment does not explicitly address multiple activities. Although this has not prevented its use for assessments of risks from multiple agents, the routine assessment of complex programs or of multiple agents acting on a site, watershed or region would be aided by use of a framework that is designed for that purpose. The framework proposed in this paper is modular with respect to the individual activities which makes the assessment more manageable and more efficient when the same activities are addressed in multiple programs or at multiple sites. It explicitly allows for analysis of indirect effects in terms of causal chains. It includes links to other risk assessments for which changes in ecological conditions are the hazardous agent. For example, changes in ecological condition may create risks to agricultural economies or to the cultural resource values of a site. Finally, the framework includes a standard approach to estimating the combined effects of the multiple agents acting on a receptor.     

NetLogoR: a package to build and run spatially explicit agent‐based models in R

NetLogoR is an R package to build and run spatially explicit agent‐based models (SE‐ABMs) using the R language. SE‐ABMs are models that simulate the fate of entities at the individual level within a spatial context and where patterns emerge at the population level. NetLogoR follows the same framework as the NetLogo software (Wilensky 1999). Rather than a call function to use the NetLogo software, NetLogoR is a translation into the R language of the structure and functions of NetLogo. Models built with NetLogoR are written in R language and are run on the R platform; no other software or language has to be involved. NetLogoR provides new R classes to define model agent objects and functions to implement spatially explicit agent‐based models in the R environment. Users of this package benefit from the fast and easy coding provided by the highly developed NetLogo framework, coupled with the versatility, power and massive resources of the R language.     

Evolution of a multi-agent system in a cyclical environment

The synchronisation phenomena in biological systems is a current and recurring subject of scientific study. This topic, namely that of circadian clocks, served as inspiration to develop an agent-based simulation that serves the main purpose of being a proof-of-concept of the model used in the BitBang framework, that implements a modern autonomous agent model. Despite having been extensively studied, circadian clocks still have much to be investigated. Rather than wanting to learn more about the internals of this biological process, we look to study the emergence of this kind of adaptation to a daily cycle. To that end we implemented a world with a day/night cycle, and analyse the ways the agents adapt to that cycle. The results show the evolution of the agents’ ability to gather food. If we look at the total number of agents over the course of an experiment, we can pinpoint the time when reproductive technology emerges. We also show that the agents adapt to the daily cycle. This circadian rhythm can be shown by analysing the variation on the agents metabolic rate, which is affected by the variation of their movement patterns. In the experiments conducted we can observe that the metabolic rate of the agents varies according to the daily cycle.     

Software architecture definition for on-demand cloud provisioning

Cloud computing is a promising paradigm for the provisioning of IT services. Cloud computing infrastructures, such as those offered by the RESERVOIR project, aim to facilitate the deployment, management and execution of services across multiple physical locations in a seamless manner. In order for service providers to meet their quality of service objectives, it is important to examine how software architectures can be described to take full advantage of the capabilities introduced by such platforms. When dealing with software systems involving numerous loosely coupled components, architectural constraints need to be made explicit to ensure continuous operation when allocating and migrating services from one host in the Cloud to another. In addition, the need for optimising resources and minimising over-provisioning requires service providers to control the dynamic adjustment of capacity throughout the entire service lifecycle. We discuss the implications for software architecture definitions of distributed applications that are to be deployed on Clouds. In particular, we identify novel primitives to support service elasticity, co-location and other requirements, propose language abstractions for these primitives and define their behavioural semantics precisely by establishing constraints on the relationship between architecture definitions and Cloud management infrastructures using a model denotational approach in order to derive appropriate service management cycles. Using these primitives and semantic definition as a basis, we define a service management framework implementation that supports on demand cloud provisioning and present a novel monitoring framework that meets the demands of Cloud based applications.     

A framework for intelligent data acquisition and real-time database searching for shotgun proteomics

In the analysis of complex peptide mixtures by MS-based proteomics, many more peptides elute at any given time than can be identified and quantified by the mass spectrometer. This makes it desirable to optimally allocate peptide sequencing and narrow mass range quantification events. In computer science, intelligent agents are frequently used to make autonomous decisions in complex environments. Here we develop and describe a framework for intelligent data acquisition and real-time database searching and showcase selected examples. The intelligent agent is implemented in the MaxQuant computational proteomics environment, termed MaxQuant Real-Time. It analyzes data as it is acquired on the mass spectrometer, constructs isotope patterns and SILAC pair information as well as controls MS and tandem MS events based on real-time and prior MS data or external knowledge. Re-implementing a top10 method in the intelligent agent yields similar performance to the data dependent methods running on the mass spectrometer itself. We demonstrate the capabilities of MaxQuant Real-Time by creating a real-time search engine capable of identifying peptides "on-the-fly" within 30 ms, well within the time constraints of a shotgun fragmentation "topN" method. The agent can focus sequencing events onto peptides of specific interest, such as those originating from a specific gene ontology (GO) term, or peptides that are likely modified versions of already identified peptides. Finally, we demonstrate enhanced quantification of SILAC pairs whose ratios were poorly defined in survey spectra. MaxQuant Real-Time is flexible and can be applied to a large number of scenarios that would benefit from intelligent, directed data acquisition. Our framework should be especially useful for new instrument types, such as the quadrupole-Orbitrap, that are currently becoming available.