This paper demonstrates B-Fabric, an all-in-one solution for two major purposes in life sciences. On the one hand, it is a system for the integrated management of experimental data and scientific annotations. On the other hand, it is a system infrastructure supporting on-the fly coupling of user applications, and thus serving as extensible platform for fast-paced, cutting-edge, collaborative research.

Modern biology has become a science of information, analysis and prediction, coalescing into computational biology -- a single discipline at the crossroads of life sciences, informatics, and mathematics. New developments in information and communications technology as well as high-performance computing enable researchers to address new demanding scientific problems which seemed far out of reach only a few years ago. The computational requirements of most applications in computational biology differ significantly from the requirements of other users of highthroughput computing such as high energy physics. To address these needs, the SwissBioGrid initiative, a collaboration among several partner institutions with a broad spectrum of expertise, was started over a year ago. In this paper, we report on its current status and achievements as well as the lessons learned which are of interest to the wider e-Science and Grid communities.

Business processes executing in peer-to-peer environments usually invoke Web services on different, independent peers. Although peer-to-peer environments inherently lack global control, some business processes nevertheless require global transactional guarantees, i.e., atomicity and isolation applied at the level of processes. This paper introduces a new decentralized serialization graph testing protocol to ensure concurrency control and recovery in peer-to-peer environments. The uniqueness of the proposed protocol is that it ensures global correctness without relying on a global serialization graph. Essentially, each transactional process is equipped with partial knowledge that allows the transactional processes to coordinate. Globally correct execution is achieved by communication among dependent transactional processes and the peers they have accessed. In case of failures, a combination of partial backward and forward recovery is applied. Experimental results exhibit a significant performance gain over traditional distributed locking-based protocols with respect to the execution of transactions encompassing Web service requests.

Standards like SOAP, WSDL, and UDDI facilitate the proliferation of services. Based on these technologies, processes are a means to combine services to applications and to provide new value-added services. For large information systems, a centralized process engine is no longer appropriate due to limited scalability. Instead, in this paper, we propose a distributed and decentralized process engine that routes process instances directly from one peer to the next. Such a peer-to-peer process execution promises good scalability characteristics since it is able to dynamically balance the load of processes and services among all available service providers. Therefore, navigation costs only accumulate on peers that are directly involved in the execution. However, this requires sophisticated strategies for the replication of meta-data for peer-to-peer process execution. Especially, replication mechanisms should avoid frequent accesses to global information repositories. In our system, called OSIRIS (Open Service Infrastructure for Reliable and Integrated Process Support), we deploy a publish/subscribe-based replication scheme together with freshness predicates to significantly reduce replication costs. This way, OSIRIS can support process-based applications in a dynamically evolving system without limiting scalability and correctness. Experiments have shown very promising results with respect to scalability. In addition, OSIRIS provides a flexible infrastructure that can be extended seamlessly in a modular way. This paper demonstrates the extension towards distributed concurrency control.

The transaction closure framework provides means to describe and reason about different kind of dependencies between interrelated transactions. In this paper, we investigate execution dependencies for describing certain control flows among related transactions of a transaction closure. In particular, we consider the transitivity property for all kinds of transaction execution dependencies and present a complete and minimal set of rules for reasoning about the transitivity of execution dependencies. Furthermore, we analyze the relationship between execution and termination dependencies and point out that some dependency combinations are incompatible. Using derived transitive dependencies, we are able to conclude how arbitrary transactions of a transaction closure are transitively interrelated and, thus, to detect contradictory dependency specifications as well as superfluous transactions.

Article An incremental approach to schema integration by refining extensional relationships Share on Authors: Ingo Schmitt Otto-von-Guericke-Universität Magdeburg, Institut für Technische und Betriebliche Informationssysteme, Postfach 4120, D-39016 Magdeburg, Germany Otto-von-Guericke-Universität Magdeburg, Institut für Technische und Betriebliche Informationssysteme, Postfach 4120, D-39016 Magdeburg, GermanyView Profile , Can Türker Otto-von-Guericke-Universität Magdeburg, Institut für Technische und Betriebliche Informationssysteme, Postfach 4120, D-39016 Magdeburg, Germany Otto-von-Guericke-Universität Magdeburg, Institut für Technische und Betriebliche Informationssysteme, Postfach 4120, D-39016 Magdeburg, GermanyView Profile Authors Info & Claims CIKM '98: Proceedings of the seventh international conference on Information and knowledge managementNovember 1998 Pages 322–330https://doi.org/10.1145/288627.288673Online:01 November 1998Publication History 3citation356DownloadsMetricsTotal Citations3Total Downloads356Last 12 Months1Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access

Activities of advanced applications can be modeled by interrelated transactions. These relations can be described by different kinds of transaction dependencies. The notion of transaction closure is a generalization of nested transactions providing means to describe complex activities such as transactional workflows. In this paper our main focus lies on execution dependencies for describing certain control flows among related transactions of transaction closures. In particular we consider the transitivity property for all kinds of transaction execution dependencies and discuss their relationship to other kinds of dependencies such as transaction termination dependencies. We point out that some of these dependency combinations are incompatible. As a result we present rules for reasoning about the transitivity of execution dependencies. Thus, we are able to conclude how arbitrary transactions of a transaction closure are transitively interrelated.

Complex applications consist of a large set of transactions which are interrelated. There are different kinds of dependencies among transactions of a complex application, e.g. termination or execution dependencies which are constraints on the occurrence of significant transaction events. The authors analyze a set of (orthogonal) transaction dependencies. They do not follow traditional approaches which consider advanced transaction structures as a certain kind of nested transactions. They introduce the notion of transaction closure as a generalization of nested transactions. A transaction closure comprises all transactions which are (transitively) initiated by one (root) transaction. By specifying dependencies among transactions of a transaction closure they are then able to define well-known transaction structures like nested transactions as well as advanced activity structures, e.g. workflows, in a common framework. In particular they consider the transitivity property for all kinds of transaction dependencies discussed in the paper. Thus, they are able to conclude how two arbitrary transactions are transitively interrelated. This issue is fundamental for understanding the entire semantics of a complex application.