R. Mark Greenwood

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.

A suite of DAML+OIL ontologies to describe bioinformatics web services and data

The growing quantity and distribution of bioinformatics resources means that finding and utilizing them requires a great deal of expert knowledge, especially as many resources need to be tied together into a workflow to accomplish a useful goal. We want to formally capture at least some of this knowledge within a virtual workbench and middleware framework to assist a wider range of biologists in utilizing these resources. Different activities require different representations of knowledge. Finding or substituting a service within a workflow is often best supported by a classification. Marshalling and configuring services is best accomplished using a formal description. Both representations are highly interdependent and maintaining consistency between the two by hand is difficult. We report on a description logic approach using the web ontology language DAML+OIL that uses property based service descriptions. The ontology is founded on DAML-S to dynamically create service classifications. These classifications are then used to support semantic service matching and discovery in a large grid based middleware project . We describe the extensions necessary to DAML-S in order to support bioinformatics service description; the utility of DAML+OIL in creating dynamic classifications based on formal descriptions; and the implementation of a DAML+OIL ontology service to support partial user-driven service matching and composition.

Using semantic web technologies for representing E-science provenance

Life science researchers increasingly rely on the web as a primary source of data, forcing them to apply the same rigor to its use as to an experiment in the laboratory. The Grid project is developing the use of workflows to explicitly capture web-based procedures, and provenance to describe how and why results were produced. Experience within Grid has shown that this provenance metadata is formed from a complex web of heterogenous resources that impact on the production of a result. Therefore we have explored the use of Semantic Web technologies such as RDF, and ontologies to support its representation and used existing initiatives such as Jena and LSID, to generate and store such material. The effective presentation of complex RDF graphs is challenging. Haystack has been used to provide multiple views of provenance metadata that can be further annotated. This work therefore forms a case study showing how existing Semantic Web tools can effectively support the emerging requirements of life science research.

Automating experiments using semantic data in a bioinformatics grid

The transition from laboratory science to in silico e-science has facilitated a paradigmatic shift in the way we conduct modern science. We can use computationally based analytical models to simulate and investigate scientific questions such as those posed by high-energy physics and bioinformatics, yielding high-quality results and discoveries at an unprecedented rate. However, while experimental media have changed, the scientific methodologies and processes we choose for conducting experiments are still relevant. As in the lab environment, experimental methodology requires samples to undergo several processing stages. The staging of operations is what constitutes the in silico experimental process. The use of workflows formalizes earlier ad hoc approaches for representing experimental methodology. We can represent the stages of in silico experiments formally as a set of services to invoke.

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.

A framework for supporting dynamic systems co-evolution

Abstract Businesses and their supporting software evolve to accommodate the constant revision and re-negotiation of commercial goals, and to intercept the potential of new technology. We have adopted the term co-evolution to describe the concept of the business and the software evolving sympathetically, but at potentially different rates. More generally, we extend co-evolution to accommodate wide-informatics systems, that are assembled from parts that co-evolve with each other and their environment, and whose behavior is potentially emergent. Typically these are long-lived systems in which dynamic co-evolution, whereby a system evolves as part of its own execution in reaction to both expected and unexpected events, is the only feasible option for change. Examples of such systems include continuously running business process models, sensor nets, grid applications, self-adapting/tuning systems, peer-to-peer routing systems, control systems, autonomic systems, and pervasive computing applications. The contribution of this paper comprises: a study of the intrinsic nature of dynamic co-evolving systems; the derivation of a set of intrinsic requirements; a description of a model and a set of technologies, new and extant, to meet these intrinsic requirements; and illustrations of how these technologies may be implemented within an architecture description language (ArchWare ADL) and a conventional programming language (Java). The model and technologies address three topics: structuring for dynamic co-evolution, incremental design, and adapting dynamic co-evolving systems. The combination yields a framework that can describe the system’s specification, the executing software and the reflective evolutionary mechanisms within a single computational domain in which all three may evolve in tandem.

A software architecture approach for structuring autonomic systems

Autonomic systems manage themselves given high-level objectives by their administrators. They utilise feedback from their own execution and their environment to self-adapt in order to satisfy their goals. An important consideration for such systems is a structure which is conducive to self-management. This paper presents a structuring methodology for autonomic systems which explicitly models self-adaptation while separating functionality and evolution. Our contribution is a software architecture-based framework combining an architecture description language based on π-calculus for describing the structure and behaviour of autonomic systems, a development methodology for evolution and mechanisms for feedback and change.

An active architecture approach to dynamic systems co-evolution

The term co-evolution describes the symbiotic relationship between dynamically changing business environments and the software that supports them. Business changes create pressures on the software to evolve, and at the same time technology changes create pressures on the business to evolve. More generally, we are concerned with systems where it is neither economically nor technologically feasible to suspend the operation of the system while it is being evolved. Typically these are long-lived systems in which dynamic co-evolution, whereby a system evolves as part of its own execution in reaction to both predicted and emergent events, is the only feasible option for change. Examples of such systems include continuously running business process models, sensor nets, grid applications, self-adapting/tuning systems, routing systems, control systems, autonomic systems, and pervasive computing applications. Active architectures address both the structural and behavioural requirements of dynamic co-evolving software by modelling software architecture as part of the on-going computation, thereby allowing evolution during execution and formal checking that desired system properties are preserved through evolution. This invited paper presents results on active architectures from the Compliant System Architecture and ArchWare projects. We have designed and constructed the ArchWare-ADL, a formal, well-founded architecture description language, based on the higher-order typed &pi-calculus, which consists of a set of layers to address the requirements of active architectures. The ArchWare-ADL design principles, concepts and formal notations are presented together with its sophisticated reflective technologies for supporting active architectures and thereby dynamic co-evolution.

A Support Framework for Dynamic Organizations

This paper describes a framework that is intended to provide an infrastructure for the delivery of support for business processes-including design processes, software development processes and procurement processes. This framework has to be capable of supporting quasi-independent process model instance evolution, and to provide seamless support in this environment for the non-expert Process Manager to exploit this capability.