Type Checking Choreography Description Language
The Web Services Choreography Description Language (WS-CDL) is a W3C specification developed for the description of peer-to-peer collaborations of participants from a global viewpoint. Currently WS-CDL has no rigorous static type checking. We believe that introducing a type system will exclude many design and description errors, and ensure desirable properties of the choreography specifications. In this paper, we took a core language CDL, which covers most of the important features of the WS-CDL, and is more convenient for the study. We developed the abstract syntax and operational semantics of CDL, and defined a collection of rules which can be used to check if choreography is well-typed. Moreover, we also proved some type safety theorems for CDL in the sense that well-typed choreography cannot get stuck. We show how the use of type information can allow us to gain confidence in the correctness of choreography.

title: Semantics of BPEL4WS-Like Fault and Compensation Handling
abstract: BPEL4WS is one of the most important business process modelling languages. One distinct feature of it is the fully programmable fault and compensation handling mechanism, which allows the user to specify the compensation behaviors of processes in application-specific manners. In this paper, we present a formal operational semantics to a simplified version of BPEL4WS, with some important concepts related to fault and compensation handling proposed and discussed, especially, the compensation closure and the compensation context. We also discuss some insights into the BPEL4WS language and its implementation obtained from this study.

title: Model Checking Dynamic UML Consistency
abstract: UML is widely accepted and extensively used in software modeling. However, using different diagrams to model different aspects of a system brings the risk of inconsistency among diagrams. In this paper, we investigate an approach to check the consistency between the sequence diagrams and statechart diagrams using the SPIN model checker. To deal with the hierarchy structure of statechart diagrams, we propose a formalism called Split Automata, a variant of automata, which is helpful to bridge the statechart diagrams to SPIN efficiently. Compared with the existing work on model checking UML which do not have formal verification for their translation from UML to the model checker, we formally define the semantics and prove that the automatically translated model (i.e. Split Automata) does simulate the UML model. In this way, we can guarantee that the translated model does represent the original model.

title: Supporting Mobility in MosquitoNet
abstract: The goal of the MosquitoNet project is to provide continuous Internet connectivity to mobile hosts. Mobile hosts must be able to take advantage of the best network connectivity available in any location, whether wired or wireless. We have implemented a mobile IP system that supports seamless switching between different networks and communication devices. In contrast to previous approaches to mobile IP, we believe mobile hosts should not assume any explicit mobility support from the networks they visit, aside from basic Internet connectivity. This decision places extra responsibilities on the mobile hosts themselves. In this paper, we describe the design and implications of such a system. Measurements of our implementation show that the inherent overhead to switch networks (below 10ms) is insignificant compared to the time required to bring up a new communication device.

title: Finding Anchors for Genomic Sequence Comparison

title: Quantifier Rewriting and Equivalence Models for Quantified Horn Formulas
abstract: In this paper, quantified Horn formulas with free variables (QHORN*) are investigated. The main result is that any quantified Horn formula Φ of length |Φ| with free variables, |∀| universal quantifiers and an arbitrary number of existential quantifiers can be transformed into an equivalent formula of length O(|∀| ·|Φ|) which contains only existential quantifiers. Moreover, it is shown that quantified Horn formulas with free variables have equivalence models where every existential quantifier is associated with a monotone Boolean function. 
 
The results allow a simple representation of quantified Horn formulas as purely existentially quantified Horn formulas . An application described in the paper is to solve QHORN*-SAT in O(|∀| ·|Φ|) by using this transformation in combination with a linear-time satisfiability checker for propositional Horn formulas.

title: Scanning microarrays at multiple intensities enhances discovery of differentially expressed genes
abstract: Scanning parameters are often overlooked when optimizing microarray experiments. A scanning approach that extends the dynamic data range by acquiring multiple scans of different intensities has been developed.



Data from each of three scan intensities (low, medium, high) were analyzed separately using multiple scan and linear regression approaches to identify and compare the sets of genes that exhibit statistically significant differential expression. In the multiple scan approach only one-third of the differentially expressed genes were shared among the three intensities, and each scan intensity identified unique sets of differentially expressed genes. The set of differentially expressed genes from any one scan amounted to < 70% of the total number of genes identified in at least one scan. The average signal intensity of genes that exhibited statistically significant changes in expression was highest for the low-intensity scan and lowest for the high-intensity scan, suggesting that low-intensity scans may be best for detecting expression differences in high-signal genes, while high-intensity scans may be best for detecting expression differences in low-signal genes. Comparison of the differentially expressed genes identified in the multiple scan and linear regression approaches revealed that the multiple scan approach effectively identifies a subset of statistically significant genes that linear regression approach is unable to identify. Quantitative RT-PCR (qRT-PCR) tests demonstrated that statistically significant differences identified at all three scan intensities can be verified.


AVAILABILITY
The data presented can be viewed at http://www.ncbi.nlm.nih.gov/geo/ under GEO accession no. GSE3017.

title: A Multi-Agent System for E-Business Processes Monitoring in a Web-Based Environment
abstract: In this paper, we present a multi-agent system MAGS for the e-business processes monitoring in a web-based environment. We classify the types of agents in MAGS by their monitoring capabilities. An algorithm is given to explain the mechanism of supervising and controlling the execution of business processes. An abstract model of alerts, which can give warnings of infringement on business policies, is proposed. Access control can also be realized by MAGS, which manifests in delivering different view of the business process to different roles participate in it. Being successfully adopted in a customer service management system, MAGS has been proven flexible and practical.