Matthew Addis

Taverna: a tool for the composition and enactment of bioinformatics workflows

MOTIVATION In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. RESULTS The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by which in silico experiments can be represented as Scufl workflows using the workbench application.

On the use of agents in a BioInformatics grid

My Grid is an e-Science Grid project that aims to help biologists and bioinformaticians to perform workflow-based in silico experiments, and help them to automate the management of such workflows through personalisation, notification of change and publication of experiments. In this paper, we describe the architecture of my Grid and how it will be used by the scientist. We then show how my Grid can benefit from agents technologies. We have identified three key uses of agent technologies in my Grid: user agents, able to customize and personalise data, agent communication languages offering a generic and portable communication medium, and negotiation allowing multiple distributed entities to reach service level agreements.

An integrated content and metadata based retrieval system for art

A new approach to image retrieval is presented in the domain of museum and gallery image collections. Specialist algorithms, developed to address specific retrieval tasks, are combined with more conventional content and metadata retrieval approaches, and implemented within a distributed architecture to provide cross-collection searching and navigation in a seamless way. External systems can access the different collections using interoperability protocols and open standards, which were extended to accommodate content based as well as text based retrieval paradigms. After a brief overview of the complete system, we describe the novel design and evaluation of some of the specialist image analysis algorithms, including a method for image retrieval based on sub-image queries, retrievals based on very low quality images and retrieval using canvas crack patterns. We show how effective retrieval results can be achieved by real end-users consisting of major museums and galleries, accessing the distributed, but integrated, digital collections.

SCULPTEUR: towards a new paradigm for multimedia museum information handling

This paper describes the design and prototype implementation of a novel architecture for integrated concept, metadata and content based browsing and retrieval of museum information. The work is part of a European project involving several major galleries and the aim is to provide more versatile access to digital collections of museum artefacts, including 2-D images, 3-D models and other multimedia representations. An ontology for the museum domain, based on the CIDOC Conceptual Reference Model, is being developed as a semantic layer with references to the digital collection as instance information. A graphical concept browser is an integral component in the user interface, allowing navigation through the semantic layer, display of thumbnails, or full representations of artefacts and textual information in appropriate viewers and the invocation of conventional content based searching or combined querying. Semantic Web technologies are used in system integration to describe how tools for analysis and visualisation can be applied to different data types and sources. This supports flexible and managed formulation, execution and interpretation of the results of distributed multimedia queries. Combined searches using concepts, content and metadata can be initiated from a single user interface.

Resource discovery for dynamic clusters in computational grids

We describe a de-centralised approach to resource management and discovery, based on a community of interacting software agents. Each agent either represents a user application, a resource, or a MatchMaking service. The proposed approach can support dynamic registration of resources and user tasks, facilitating the establishment of dynamic clusters. Resource capability and task requirements are described using an object based data model, enabling new types of devices or new features in existing devices to be identified. A comparison with the Discovery and LookUp services in Jini and TSpaces is also provided.

Delivering web service coordination capability to users

As web service technology matures there is growing interest in exploiting workflow techniques to coordinate web services. Bioinformaticians are a user community who combine web resources to perform in silico experiments. These users are scientists and not information technology experts they require workflow solutions that have a low cost of entry for service users and providers. Problems satisfying these requirements with current techniques led to the development of the Simple conceptual unified flow language (Scufl). Scufl is supported by the Freefluo enactment engine [1], and the Taverna editing workbench [3]. The extensibility of Scufl, supported by these tools, means that workflows coordinating web services can be matched to how users view their problems. The Taverna workbench exploits the web to keep Scufl simple by retrieving detail from URIs when required, and by scavenging the web for services. Scufl and its tools are not bioinformatics specific. They can be exploited by other communities who require user-driven composition and execution of workflows coordinating web resources.

SCULPTEUR: Multimedia Retrieval for Museums

The paper describes the prototype design and development of a multimedia system for museums and galleries. Key elements in the system are the introduction of 3-D models of museum artefacts together with 3-D as well as 2-D content based retrieval and navigation facilities and the development of a semantic layer, centred on an ontology for museums, which aims to expose the richness of knowledge associated with the museum collections and facilitate concept based retrieval and navigation integrated with that based on content and metadata. Interoperability protocols are designed to allow external applications to access the collection and an example is given of an e-Learning facility which uses models extracted to a virtual museum.

Negotiating for software services

We are investigating how the routine use of engineering meta-applications can be made financially viable by using a software and hardware on-demand business model supported by an agent based electronic marketplace. The authors explains how their work has combined Web, agent and security technologies to create a robust and secure Internet based marketplace in which a trusted third party provides negotiation services between software application users and third party hardware and software service providers.

Integrated image content and metadata search and retrieval across multiple databases

This paper presents an updated technical overview of an integrated content and metadata-based image retrieval system used by several major art galleries in Europe including the Louvre in Paris, the Victoria and Albert Museum in London, the Uffizi Gallery in Florence and the National Gallery in London. In our approach, the subjects of a query (e.g. images, textual metadata attributes), the operators used in a query (e.g. SimilarTo, Contains, Equals) and the rules that constrain the query (e.g. SimilarTo can only be applied to Images) are all explicitly defined and published for each gallery collection. In this way, cross-collection queries are dynamically constructed and executed in a way that is automatically constrained to the capabilities of the particular image collections being searched. The application of existing, standards based, technology to integrate metadata and content based queries underpins an open standards approach to extending interoperability across multiple image databases.

The Significance of Storage in the “Cost of Risk” of Digital Preservation

As storage costs drop, storage is becoming the lowest cost in a digital repository – and the biggest risk. We examine current modelling of costs and risks in digital preservation, concentrating on the Total Cost of Risk when using digital storage systems for preserving audiovisual material. We present a managed approach to preservation, and the vital role of storage and show how planning for long-term preservation of data should consider the risks involved in using digital storage technology. Gaps in information necessary for accurate modeling – and planning – are presented. We call for new functionality to support recovery of files with errors, to eliminate the all-or-nothing approach of current IT systems, reduce the impact of failures of digital storage technology and mitigate against loss of digital data.