Guest Editors\u27 Introduction

This Supplement includes a selection of papers presented at the 7th International Symposium on Bioinformatics Research and Application (ISBRA), which was held on May 27-29, 2011 at Central South University in Changsha, China. The technical program of the symposium included 36 extended abstracts presented orally and published in volume 6674 of Springer Verlag’s Lecture Notes in Bioinformatics series. Additionally, the program included 38 short abstracts presented either orally or as posters. Authors of both extended and short abstracts presented at the symposium were invited to submit full versions of their work to this Supplement. Following a rigorous review process, 19 of the 40 full papers submitted were selected for publication. Selected papers cover a broad range of bioinformatics topics, ranging from algorithms for structural biology to phylogenetics and biological networks

SyD: A Middleware Testbed for Collaborative Applications over Small Heterogeneous Devices and Data Stores

Abstract. Currently, it is possible to develop a collaborative application running on a collection of heterogeneous, possibly mobile, devices, each potentially hosting data stores, using existing middleware technologies such as JXTA, BREW, compact.NET and J2ME. However, they require too many ad-hoc techniques as well as cumbersome and time-consuming programming. Our System on Mobile Devices (SyD) middleware, on the other hand, has a modular architecture that makes such application de-velopment very systematic and streamlined. The architecture supports transactions over mobile data stores, with a range of remote group invo-cation options and embedded interdependencies among such data store objects. The architecture further provides a persistent uniform object view, group transaction with Quality of Service (QoS) speci¯cations, and XML vocabulary for inter-device communication. This paper presents the basic SyD concepts, introduces the architecture and the design of the SyD middleware and its components. We also provide guidelines fo

Real Time Fuzzy Personalized Web Stock Information Agent

The real time fuzzy personalized stock information agent is designed based on fuzzy logic, intelligent agent, personalization, Jakarta-Tomcat-3.2.1 (Web sever) and Microsoft SQL Server 7.0 (database). In addition, a variety of languages, including Java, JSP (Java Sever Page), HTML, Java Servlet, XML, XSL (Extensible Stylesheet Language) are also used. The smart agent enables the users to create their own portfolios that contain the real time watch list of personalized stocks. The application refreshes each stock data in real time by accessing the appropriate database available on the Internet. This application enables the user to get accurate, real time information of a preselected list of favorite stocks. Using fuzzy reasoning, the Web stock agent is capable of ranking the “top 10 stocks” based on their real time stock information. 1

Enforcing Interdependencies and Executing Transactions Atomically over Autonomous Mobile Data Stores Using SyD Link Technology

System of Mobile Devices (SyD) is a middleware we developed that can be used for implementing collaborative, mobile, and distributed applications over heterogeneous devices, data stores, and computing environments. Current prototype implementation of SyD consists of five modules. These modules provide ease of programming in the areas of distributed communication, remote method invocation, service publication and discovery, directory services, distributed service invocation and aggregation, event handling, collaborative link creation and enforcement. A central module is SyDLink, which allows SyD-based applications to create "coordination" links. Coordination links represent dependencies among heterogeneous devices and application components. Based on the underlying eventand -trigger mechanism, they allow automatic updates as well as real-time enforcement of global constraints and interdependencies. SyDLink objects provide the underlying mechanism in SyD to enforce atomic execution of distributed transactions. We explain and demonstrate the use of SyDLink objects via a running example, a collaborative SyD calendar application, throughout the paper