Justin Ferris

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.

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.

Grid-Enabled Workflows for Industrial Product Design

This paper presents a generic approach for developing and using Grid-based workflow technology for enabling cross-organizational engineering applications. Using industrial product design examples from the automotive and aerospace industries we highlight the main requirements and challenges addressed by our approach and describe how it can be used for enabling interoperability between heterogeneous workflow engines.

Panoply of utilities in Taverna

The Taverna e-Science Workbench is a central component of myGrid, a loosely coupled suite of middleware services designed to support in silico experiments in biology. Taverna enables the construction and enactment of complex workflows over resources on local and remote machines, allowing the automation of otherwise labour-intensive multi-step bioinformatics tasks. As the Taverna user community has grown, so has the demand for new features and additions. This paper outlines the functional requirements that have become apparent over the last year of working with domain scientists, along with the solutions implemented in both the Taverna workbench and the Freefluo enactment engine to address concerns relating to workflow construction and enactment, respectively

Business Value Chains in Real-Time On-Line Interactive Applications

Grid infrastructure are already being used in the on-line gaming sector to provide large-scale game hosting in a business context. However, the game platforms and infrastructures used do not take advantage of the potential for rich business networks to support indefinite scaling within single game instances, or to simplify the problem of managing the quality of experience and access rights for end customers. The European edutain@grid research project is developing an infrastructure for realising such business networks using bipartite Service Level Agreements. This paper describes the analysis of business value chains and SLA terms for the initial implementation, and provides insights into how these should be formulated, and what challenges this presents to Grid infrastructure implementers.

A Dynamic Orchestration Model for Future Internet Applications

Society and business are demanding systems that can securely and cost-effectively exploit opportunities presented by an Internet of Services. To achieve this goal a system must dynamically adapt to its environment and consider multiple and shifting stakeholder concerns such as application functionality, policies and business processes. In this paper we describe a dynamic orchestration model called the Virtual Infrastructure Model (VIM) which allows consumers to develop service-oriented systems that adapt to the needs of different business actors. It is based on the idea that adaptive workflow and dynamic binding to services can facilitate abstraction of both business processes and requisite interactions with the underlying infrastructure. Key requirements for federated orchestration are addressed including runtime service binding, secure and accountable dynamic procurement, infrastructure adaption, and separation of stakeholder concerns. The VIM is a fundamental component of the Next Generation Grid Architecture developed in the context of the EU funded NextGRID project.