1,721,191 research outputs found
Agent-Oriented Data Curation in Bioinformatics
No full textThe practitioners of bioinformatics require increasing sophistication from their software tools to take into account the particular characteristics that make their domain complex. For example, there is a great variation of experience of researchers, from novices who would like guidance from experts in the best resources to use to experts that wish to take greater management control of the tools used in their experiments. Also, the range of available, and conflicting, data formats is growing and there is a desire to automate the many trivial manual stages of in-silico experiments. Agent-oriented software development is one approach to tackling the design of complex applications. In this paper, we argue that, in fact, agent-oriented development is a particularly well-suited approach to developing bioinformatics tools that take into account the wider domain characteristics. To illustrate this, we design a data curation tool, which manages the format of experimental data, extend it to better account for the extra requirements placed by the domain characteristics, and show how the characteristics lead to a system well suited to an agent-oriented view
Open Systems Design Using Agent Interactions
No full textAs software requirements grow increasingly complex, the need to connect to and re-use existing, tested software, grows with it. Open systems, such as the Internet, aid this process by connecting together software services provided by a range of organisations, and the distributed nature of the system allows the services to be regularly updated and improved. Applications can be deployed within the open systems that opportunistically attempt to make use of the best functionality available at any one time. Agent-based systems have been proposed as an ideal way to implement such applications, due to their flexibility and distributed control. However, a balance must be kept between acting opportunistically and ensuring that each application operates to the standards demanded by the application requirements. Determining whether an application will perform to its requirements necessitates justifying the design decisions made in creating it. Our goal is to provide application developers with the means to create justified designs for opportunistic applications. The main contribution of this thesis is a software engineering methodology, agent interaction analysis, based on a set of independently valuable techniques we have developed. The first of these is a novel approach to modelling applications as being instantiated by a set of agent interactions, allowing such applications to be described with minimal restrictions on their implemented structure. Second, we provide a technique, based on design patterns, for comparing mechanisms for instantiating parts of multi-agent system. Finally, we provide an approach to more detailed analysis and comparison of coordination mechanisms
Electronically Querying for the Provenance of Entities
Full text linkThe provenance of entities, whether electronic data or physical artefacts, is crucial information in practically all domains, including science, business and art. The increased use of software in automating activities provides the opportunity to add greatly to the amount we can know about an entity’s history and the process by which it came to be as it is. However, it also presents difficulties: querying for the provenance of an entity could potentially return detailed information stretching back to the beginning of time, and most of it irrelevant to the querier. In this paper, we define the concept of provenance query and describe techniques that allow us to perform scoped provenance queries
MyGrid Notification Service Alpha Release 1.0 WSDL Interface Description (Draft 0.2)
No full textMyGrid notification service alpha 1.0 is described in WSDL. The WSDL document specifies the data types, the messages and the ports the service exposes. The section of the WSDL document is comprised of abstract definitions where SOAP messages are defined in a platform- and language-independent manner. In the bottom section of the WSDL document the site-specific matters such as protocol and serialization are defined. This document provides a detail explanation of notification service interfaces as specified in the WSDL document
MyGrid Notification Service Alpha 1.0 Quick Start
No full textThis manual serves as a quick start to the notification service alpha 1.0, covering installation, building, configuration and deployment
The requirements of using provenance in e-Science experiments
Full text linkIn e-Science experiments, it is vital to record the experimental process for later use such as in interpreting results, verifying that the correct process took place or tracing where data came from. The process that led to some data is called the provenance of that data, and a provenance architecture is the software architecture for a system that will provide the necessary functionality to record, store and use process documentation to determine the provenance of data items. However, there has been little principled analysis of what is actually required of a provenance architecture, so it is impossible to determine the functionality they would ideally support. In this paper, we present use cases for a provenance architecture from current experiments in biology, chemistry, physics and computer science, and analyse the use cases to determine the technical requirements of a generic, technology and applicationindependent architecture. We propose an architecture that meets these requirements, analyse its features compared with other approaches and evaluate a preliminary implementation by attempting to realise two of the use cases
MyGrid Notification Service Technical Requirements and Descriptions (Draft 0.3)
No full textThis document provides a high level technical requirements of myGrid notification service. It describes the ideas, principles and procedures that will be implemented in order to meet the functional requirements
The requirements of recording and using provenance in e-Science experiments
No full textIn e-Science experiments, it is vital to record the experimental process for later use such as in interpreting results, verifying that the correct process took place or tracing where data came from. The process that led to some data is called the provenance of that data, and a provenance architecture is the software architecture for a system that will provide the necessary functionality to record, store and use process documentation to determine the provenance of data items. However, there has been little principled analysis of what is actually required of a provenance architecture, so it is impossible to determine the functionality they would ideally support. In this paper, we present use cases for a provenance architecture from current experiments in biology, chemistry, physics and computer science, and analyse the use cases to determine the technical requirements of a generic, application-independent architecture. We propose an architecture that meets these requirements and evaluate a preliminary implementation by attempting to realise two of the use cases
Architecture for Provenance Systems
No full textThis document covers the logical and process architectures of provenance systems. The logical architecture identifies key roles and their interactions, whereas the process architecture discusses distribution and security. A fundamental aspect of our presentation is its technology-independent nature, which makes it reusable: the principles that are exposed in this document may be applied to different technologies
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