Adaptive offloading inference for delivering applications in pervasive computing environments
Pervasive computing allows a user to access an application on heterogeneous devices continuously and consistently. However it is challenging to deliver complex applications on resource-constrained mobile devices, such as cellular telephones and PDA. Different approaches, such as application-based or system-based adaptations, have been proposed to address the problem. However existing solutions often require degrading application fidelity. We believe that this problem can be overcome by dynamically partitioning the application and offloading part of the application execution to a powerful nearby surrogate. This will enable pervasive application delivery to be realized without significant fidelity degradation or expensive application rewriting. Because pervasive computing environments are highly dynamic, the runtime offloading system needs to adapt to both application execution patterns and resource fluctuations. Using the fuzzy control model, we have developed an offloading inference engine to adaptively solve two key decision-making problems during runtime offloading: (1) timely triggering of adaptive offloading, and (2) intelligent selection of an application partitioning policy. Extensive trace-driven evaluations show the effectiveness of the offloading inference engine.

title: An overlay based QoS-aware voice-over-IP conferencing system
abstract: Ubiquitous IP telephony has become a feasible Internet service, and it is expected to meet the quality standards of traditional telephone services. The work presents a distributed voice-over-IP (VoIP) conferencing system called Venus that is implemented as a composable application-level service overlay network. Compared to the traditional centralized approach, Venus achieves better scalability and resource utilization by efficiently aggregating resources across distributed voice mixers. Moreover, Venus provides multi-constrained quality-of-service (QoS) provisioning by establishing each conferencing session based on multiple QoS constraints (e.g., delay, loss rate) and resource requirements (e.g., bandwidth, audio channels). Venus provides a failure resilient VoIP conferencing service by leveraging the fast failure recovery capability of the application-level service overlay network. Large-scale simulation results illustrate the efficiency of the Venus system.

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: 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: Visual QoS programming environment for ubiquitous multimedia services
abstract: 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: 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: DRTF: a database of rice transcription factors
abstract: DRTF contains 2025 putative transcription factors (TFs) in Oryza sativa L. ssp. indica and 2384 in ssp. japonica, distributed in 63 families, identified by computational prediction and manual curation. It includes detailed annotations of each TF including sequence features, functional domains, Gene Ontology assignment, chromosomal localization, EST and microarray expression information, as well as multiple sequence alignment of the DNA-binding domains for each TF family. The database can be browsed and searched with a user-friendly web interface.


AVAILABILITY
DRTF is available at http://drtf.cbi.pku.edu.cn

title: Evolutionary analysis of functional divergence in TGF- signaling pathway
abstract: TGF-β cytokines and their interacting receptors form an intricate signaling network and play important roles in cell differentiation and development. Members in gene families involved in this complicated pathway are usually conserved in sequence but distinct in temporal and tissue-specific expression. Starting from an evolutionary perspective, we have statistically tested the functional divergence in major pathway components, targeted the critical amino acid residues responsible for functional divergence. Our results show that altered functional constraints is a common pattern in the evolution of TGF-β pathway. Moreover, we have found the correlation between structural divergence and functional divergence in the extracellular ligand-binding domain of Type II receptors. This study helps understand the complex intrinsic mechanisms of signaling.

title: Algorithms for Multiple Genome Rearrangement by Signed Reversals
abstract: We discuss a multiple genome rearrangement problem by signed reversals: Given a collection of genomes, we generate them in the minimum number of signed reversals. It is NP-hard and equivalent to finding an optimal Steiner tree to connect the genomes by reversal paths. We design two algorithms to find the optimal Steiner nodes of the problem: Neighbor-perturbing algorithm and branch-and-bound algorithm. The first one is a polynomial running time approximation algorithm. It searches for the optimal Steiner nodes by perturbing initial Steiner nodes nearby their neighborhoods and improving them better and better until convergence. The second one is an exact exponential running time algorithm for a median problem. It finds the optimal Steiner node by checking all candidates that satisfy the necessary conditions for optimal Steiner nodes. We implement the algorithms into two programs respectively and show by experimental examples that they are more efficient than other similar ones, such as GRAPPA, BPAnalysis, and MGR, etc.

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.

title: Global Conformal Parameterization