Optimal Component Composition for Scalable Stream Processing
Stream processing has become increasingly important with emergence of stream applications such as audio/video surveillance, stock price tracing, and sensor data analysis. A challenging problem is to provide optimal component composition in a distributed stream processing environment. The goal of optimal component composition is to achieve load balancing subject to multiple function, resource, and quality-of-service (QoS) constraints while composing stream applications. In this paper, we present an adaptive composition probing (ACP) approach to the problem. Different from previous work, ACP provides a new hybrid approach that combines distributed composition probing with coarse-grain global state management. Guided by the coarse-grain global state information, ACP selectively probes a subset of candidate components to discover an approximately optimal component composition. Further, ACP is self-tuning, which can adoptively adjust the number of probes to maintain a specified composition performance target (i.e., composition success rate) in a dynamic stream environment. While the optimal component composition problem is NP-hard, our ACP approach provides an adaptive polynomial approximation solution. We have conducted extensive simulation experiments to show the efficiency, scalability, and adaptability of the ACP approach by comparing with other alternative solutions

title: An XML-based Quality of Service Enabling Language for the Web
abstract: In this paper, we introduce an XML-based hierarchical QoS markup language, called HQML, to enhance distributed multimedia applications on the World Wide Web (WWW) with quality of service (QoS) capability. The design ofHQML is based on two observations: (1) the absence of a systematic QoS specification language, that can be used by distributed multimedia applications on the WWW to utilize the state-of-the-art QoS management technology and (2) the power and popularity of XML to deliver richly structured contents over the Web. HQML allows distributed multimedia applications to specify all kinds of application-specific QoS policies and requirements. During runtime, the HQML Executor translates the HQML file into desired data structures and cooperates with the QoS proxies that assist applications in end-to-end QoS negotiation, setup and enforcement. In order to make QoS services tailored toward user preferences and meet the challenges of uncertainty in the distributed heterogeneous environments, the design of HQML is featured as interactive andflexible . In order to allow application developers to create HQML specifications correctly and easily, we have designed and developed a unified visual QoS programming environment, called QoSTalk. In QoSTalk, we adopt a grammatical approach to perform consistency check on the visual QoS specifications and generate HQML files automatically. Finally, we introduce the distributed QoS compiler, which performs the automatic mappings between application- and resource-level QoS parameters to relieve the application developer of the burden of dealing with low-level QoS specifications.

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: 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: Adaptive offloading inference for delivering applications in pervasive computing environments
abstract: 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: 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: 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: Performance evaluation of DCCP: A focus on smoothness and TCP-friendliness
abstract: Recent years have seen dramatic increases of the use of multimedia applications on the Internet, which typically either lack congestion control or use proprietary congestion control mechanisms. This can easily cause congestion collapse or compatibility problems. Datagram Congestion Control Protocol (Dccp) fills the gap betweenUdp andTcp, featuring congestion control rather than reliability for packet-switched rich content delivery with high degree of flexibility. We present aDccp model designed and implemented withOpnet Modeler, and the experiments and evaluation focused on largely the smoothness of the data rates, and the fairness between concurrentDccp flows andTcp flows. We foundDccp-ccid3 demonstrates stable data rates under different scenarios, and the fairness betweenDccp andTcp is only achieved under certain conditions. We also validated that the throughput ofDccp-Ccid3 is proportional to the average packet size, and relatively fixed packet size is critical for the optimal operation ofDccp. Problems in the slow start phase and insufficient receiver buffer size were identified and we hereby proposed solutions on this.RésuméLe nombre d’applications multimédias sur l’internet a considérablement augmenté ces dernières années. Ces applications généralement ne gèrent pas les congestions ou bien utilisent des mécanismes de contrôle propriétaires. Il peut en résulter facilement des congestions graves ou des problèmes d’incompatibilité. Le protocoleDccp (Datagram Congestion Control Protocol) se positionne entreUdp etTcp puisqu ’il fournit, pour des paquets multimédias, un contrôle de congestion hautement flexible mais sans la fiabilité de délivrance. Cet article présente un modèleDccp conçu et implémenté avec le simulateurOpnet. Les expérimentations et les analyses portent principalement sur le lissage des débits et l’équité entre des fluxDccp etTcp concurrents. On montre queDccp-Ccid3 affiche des débits stables sous divers scénarios et que l’équité entreDccp etTcp n’est atteinte que sous certaines conditions. On valide également que le débit deDccp-Ccid3 est proportionnel à la taille moyenne des paquets et que le fait d’avoir des paquets de taille relativement constante est un facteur essentiel pour un fonctionnement optimal deDccp. Les problèmes pendant la phase de démarrage lent et ceux dus à une mémoire tampon insuffisante côté récepteur sont également analysés et résolus.

title: Polyhedral Geometry and the Two-Plane Parameterization
abstract: Recently the light-field and lumigraph systems have been proposed as general methods of representing the visual information present in a scene. These methods represent this information as a 4D function of light over the domain of directed lines. These systems use the intersection points of the lines on two planes to parameterize the lines in space. This paper explores the structure of the two-plane parameterization in detail. In particular we analyze the association between the geometry of the scene and subsets of the 4D data. The answers to these questions are essential to understanding the relationship between a lumigraph, and the geometry that it attempts to represent. This knowledge is potentially important for a variety of applications such as extracting shape from lumigraph data, and lumigraph compression.

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: 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.