Visual QoS programming environment for ubiquitous multimedia services
The provision of distributed multimedia services is becoming mobile and ubiquitous. Different multimedia services require application-specific Quality of Service (QoS). In this paper, we present QoSTalk, a unified component-based programming environment that allows application developers to specify different application-specific QoS requirements easily. In QoSTalk, we adopt a hierarchical approach to model application configuration graphs for different distributed multimedia services. We design and implement the XML-based Hierarchical QoS Markup Language, called HQML, to describe the hierarchical configuration graph as well as other application-specific QoS requirements and policies. QoSTalk promotes the separation of concerns in developing QoS-aware ubiquitous multimedia applications and thus enables easy programming of QoS-aware applications, running on top of a unified QoS-aware middleware framework. We have prototyped the QoSTalk in Java and CORBA. Our case studies with several multimedia applications show that QoSTalk effectively fills the gap for application developers between the very general facilities provided by the QoS-aware middleware and different kinds of distributed multimedia applications.

title: On Composing Stream Applications in Peer-to-Peer Environments
abstract: Stream processing has become increasingly important as many emerging applications call for continuous real-time processing over data streams, such as voice-over-IP telephony, security surveillance, and sensor data analysis. In this paper, we propose a composable stream processing system for cooperative peer-to-peer environments. The system can dynamically select and compose stream processing elements located on different peers into user desired applications. We investigate multiple alternative approaches to composing stream applications: 1) global-state-based centralized versus local-state-based distributed algorithms for initially composing stream applications at setup phase. The centralized algorithm performs periodical global state maintenance while the distributed algorithm performs on-demand state collection. 2) Reactive versus proactive failure recovery schemes for maintaining composed stream applications during runtime. The reactive failure recovery algorithm dynamically recomposes a new stream application upon failures while the proactive approach maintains a number of backup compositions for failure recovery. We conduct both theoretical analysis and experimental evaluations to study the properties of different approaches. Our study illustrates the performance and overhead trade-offs among different design alternatives, which can provide important guidance for selecting proper algorithms to compose stream applications in cooperative peer-to-peer environments

title: Dynamic QoS-aware multimedia service configuration in ubiquitous computing environments
abstract: Ubiquitous computing promotes the proliferation of various stationary, embedded and mobile devices interconnected by heterogeneous networks. It leads to a highly dynamic distributed system with many devices and services coming and going frequently. Many emerging distributed multimedia applications are being deployed in such a computing environment. In order to make the experience for a user truly seamless and to provide soft performance guarantees, we must meet the following challenges: (1) users should be able to perform tasks continuously, despite changes of resources, devices and locations; (2) users should be able to efficiently utilize all accessible resources within runtime environments to receive the best possible Quality-of-Service (QoS). In this paper, we propose an integrated QoS-aware service configuration model to address the above problems. The configuration model includes two tiers: (1) service composition tier, which is responsible for choosing and composing current available service components appropriately and coordinating arbitrary interactions between them to achieve the user's objectives; and (2) service distribution tier which is responsible for dividing an application into several partitions and distributing them to different available devices appropriately. Our initial experimental results based on both prototype and simulations show the soundness of our model and algorithms.

title: A programming framework for quality-aware ubiquitous multimedia applications
abstract: Ubiquitous computing promises a computing environment that seamlessly and pervasively delivers applications to the user, despite changes of resources, devices, and locations. However, few ubiquitous multimedia applications (UMAs) exist up-to-date. One of the main reasons lies in the fact that it is difficult and error-prone to build a UMA which is mobile and deployable in different ubiquitous environments, and still provides acceptable application-specific Quality-of-Service (QoS) guarantees. In this paper, we present the design and implementation of a novel programming framework, called 'QCompiler" to address the challenges. The framework includes (1) a high-level application specification for the application developer to easily write a UMA with specific quality, mobility, and ubiquity supports, (2) a meta-data compilation, which provides automated consistency checks, translations, and substitutions, to relieve the application developer from dealing with complex programming related to quality, mobility, and ubiquity, (3) a binding, which prepares a quality-aware specification to be executable, in a specific deployment environment, and (4)a run-time meta-data execution, utilizing the meta-data compilation's results, to manage and control a quality-aware multimedia application. As a case study, we apply the programming framework to build a mobile Video-on-Demand (VoD) application. The experimental results show tradeoffs between easiness and flexibility to develop and deploy UMA, and overheads during UMA instantiation and adaptation.

title: QoS-assured service composition in managed service overlay networks
abstract: Many value-added and content delivery services are being offered via service level agreements (SLAs). These services can be interconnected to form a service overlay network (SON) over the Internet. Service composition in SON has emerged as a cost-effective approach to quickly creating new services. Previous research has addressed the reliability, adaptability, and compatibility issues for composed services. However little has been done to manage generic quality-of-service (QoS) provisioning for composed services, based on the SLA contracts of individual services. In this paper we present QUEST a QoS assUred composEable Service infrasTructure, to address the problem. QUEST framework provides: (1) initial service composition, which can compose a qualified service path under multiple QoS constraints (e.g., response time, availability). If multiple qualified service paths exist, QUEST chooses the best one according to the load balancing metric; and (2) dynamic service composition, which can dynamically recompose the service path to quickly recover from service outages and QoS violations. Different from the previous work, QUEST can simultaneously achieve QoS assurances and good load balancing in SON.

title: Synergy: Sharing-Aware Component Composition for Distributed Stream Processing Systems
abstract: Many emerging on-line data analysis applications require applying continuous query operations such as correlation, aggregation, and filtering to data streams in real-time. Distributed stream processing systems allow in-network stream processing to achieve better scalability and quality-of-service (QoS) provision. In this paper we present Synergy, a distributed stream processing middleware that provides sharing-aware component composition. Synergy enables efficient reuse of both data streams and processing components, while composing distributed stream processing applications with QoS demands. Synergy provides a set of fully distributed algorithms to discover and evaluate the reusability of available data streams and processing components when instantiating new stream applications. For QoS provision, Synergy performs QoS impact projection to examine whether the shared processing can cause QoS violations on currently running applications. We have implemented a prototype of the Synergy middleware and evaluated its performance on both PlanetLab and simulation testbeds. The experimental results show that Synergy can achieve much better resource utilization and QoS provision than previously proposed schemes, by judiciously sharing streams and processing components during application composition.

title: Manifold splines
abstract: Constructing splines whose parametric domain is an arbitrary manifold and effectively computing such splines in real-world applications are of fundamental importance in solid and shape modeling, geometric design, graphics, etc. This paper presents a general theoretical and computational framework, in which spline surfaces defined over planar domains can be systematically extended to manifold domains with arbitrary topology with or without boundaries. We study the affine structure of domain manifolds in depth and prove that the existence of manifold splines is equivalent to the existence of a manifold's affine atlas. Based on our theoretical breakthrough, we also develop a set of practical algorithms to generalize triangular B-spline surfaces from planar domains to manifold domains. We choose triangular B-splines mainly because of its generality and many of its attractive properties. As a result, our new spline surface defined over any manifold is a piecewise polynomial surface with high parametric continuity without the need for any patching and/or trimming operations. Through our experiments, we hope to demonstrate that our novel manifold splines are both powerful and efficient in modeling arbitrarily complicated geometry and representing continuously-varying physical quantities defined over shapes of arbitrary topology.

title: Functional Divergence in TGF-b Signaling Pathway

title: A Greedy Algorithm for Optimal Recombination
abstract: Let Σ be an alphabet and Σn denote the collection of all sequences of length n over Σ. For any s1 = ajaj+1 . . . an+s2 = b1b2 . . . bj bj+1 . . . bn ∈ Σn, a recombination of s1 and s2 at position j is defined as an operation that crosses s1 and s2 at position j and generates t1 = a1a2 . . .  . bn and t2 = b1b2 . . .  Denote A and S two collections of sequences. In this paper, we discuss generating A from S by a series of recombinations in minimum number of steps. We present a greedy algorithm for finding the optimal recombination evolutionary history from S to any tree A of sequences when |S| = 2.

title: Computational methodologies for modelling, analysis and simulation of signalling networks
abstract: This article is a critical review of computational techniques used to model, analyse and simulate signalling networks. We propose a conceptual framework, and discuss the role of signalling networks in three major areas: signal transduction, cellular rhythms and cell-to-cell communication. In order to avoid an overly abstract and general discussion, we focus on three case studies in the areas of receptor signalling and kinase cascades, cell-cycle regulation and wound healing. We report on a variety of modelling techniques and associated tools, in addition to the traditional approach based on ordinary differential equations (ODEs), which provide a range of descriptive and analytical powers. As the field matures, we expect a wider uptake of these alternative approaches for several reasons, including the need to take into account low protein copy numbers and noise and the great complexity of cellular organisation. An advantage offered by many of these alternative techniques, which have their origins in computing science, is the ability to perform sophisticated model analysis which can better relate predicted behaviour and observations.

title: Real-time service provisioning for mobile and wireless networks
abstract: As mobile devices and wireless networks are becoming ubiquitous, the interest of users to deploy real-time applications, e.g. online gaming or Voice-over-IP in such environments is also increasing. Due to the difference between traditional and wireless networks, in particular in terms of available bandwidth and network structure, the concepts used for supporting real-time applications in both networks are different. This paper gives an overview of the key technical challenges that are fundamental and need to be solved in order to easily support real-time applications in wireless and mobile environments. In a first step, issues related to service provisioning in mobile networks are discussed. This is followed by a look at the Quality of Service supported by wireless networks and possible techniques for improving it. Finally, concepts for securing the communication between the users of real-time applications in wireless and mobile networks are presented. For each of these issues, we provide a detailed analysis and an overview of the state-of-the-art. Moreover, we illustrate the main points using distributed online games as an example.