Kevin Glover

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.

ExoBuilding: Physiologically Driven Adaptive Architecture

Our surroundings are becoming infused with sensors measuring a variety of data streams about the environment, people and objects. Such data can be used to make the spaces that we inhabit responsive and interactive. Personal data in its different forms are one important data stream that such spaces are designed to respond to. In turn, one stream of personal data currently attracting high levels of interest in the HCI community is physiological data (e.g., heart rate, electrodermal activity), but this has seen little consideration in building architecture or the design of responsive environments. In this context, we developed a prototype mapping a single occupant’s respiration to its size and form, while it also sonifies their heartbeat. The result is a breathing building prototype, formative trials of which suggested that it triggers behavioral and physiological adaptations in inhabitants without giving them instructions and it is perceived as a relaxing experience. In this paper, we present and discuss the results of a controlled study of this prototype, comparing three conditions: the static prototype, regular movement and sonification and a biofeedback condition, where the occupant’s physiological data directly drives the prototype and presents this data back to them. The study confirmed that the biofeedback condition does indeed trigger behavioral changes and changes in participants’ physiology, resulting in lower respiration rates as well as higher respiration amplitudes, respiration to heart rate coherence and lower frequency heart rate variability. Self-reported state of relaxation is more dependent on inhabitant preferences, their knowledge of physiological data and whether they found space to ‘let go’. We conclude with a discussion of ExoBuilding as an immersive but also sharable biofeedback training interface and the wider potential of this approach to making buildings adapt to their inhabitants.

An information plane architecture supporting home network management

Home networks have evolved to become small-scale versions of enterprise networks. The tools for visualizing and managing such networks are primitive and continue to require networked systems expertise on the part of the home user. As a result, non-expert home users must manually manage non-obvious aspects of the network - e.g., MAC address filtering, network masks, and firewall rules, using these primitive tools. The Homework information plane architecture uses stream database concepts to generate derived events from streams of raw events. This supports a variety of visualization and monitoring techniques, and also enables construction of a closed-loop, policy-based management system. This paper describes the information plane architecture and its associated policy-based management infrastructure. Exemplar visualization and closed-loop management applications enabled by the resulting system (tuned to the skills of non-expert home users) are discussed.

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

Contextualised workflow execution in mygrid

e-Scientists stand to benefit from tools and environments that either hide, or help to manage, the inherent complexity involved in accessing and making concerted use of the diverse resources that might be used as part of an in silico experiment. This paper illustrates the benefits that derive from the provision of integrated access to contextual information that links the phases of a problem-solving activity, so that the steps of a solution do not happen in isolation, but rather as the components of a coherent whole. Experiences with myGrid workflow execution environment (Taverna) are presented, where an information model provides the conceptual basis for contextualisation. This information model describes key characteristics that are shared by many e-Science activities, and is used both to organise the scientists personal data resources, and to support data sharing and capture within the myGrid environment.

ExoBuilding: breathing life into architecture

ExoBuilding explores the novel design space that emerges when an individuals physiological data and the fabric of building architecture are linked. In its current form ExoBuilding is a tent-like structure that externalises a persons physiological data in an immersive and visceral way. This is achieved by mapping abdominal breathing to its shape and size, displaying heart beat through sound and light effects and mapping electro dermal activity to a projection on the tent fabric. The research is positioned in relation to previous work and the iterative development of ExoBuilding from to-scale to full-size prototype is described. The design process, feedback gathered alongside and observations allow the discussion of wider issues: the different scales possible, the temporal nature of the data, ownership and ambiguity of that data, ranges of control and the aggregation of data in a building context. This leads to the presentation of directions for future research at this exciting boundary between Architecture, HCI and medical science.

Accountable Artefacts: The Case of the Carolan Guitar

We explore how physical artefacts can be connected to digital records of where they have been, who they have encountered and what has happened to them, and how this can enhance their meaning and utility. We describe how a travelling technology probe in the form of an augmented acoustic guitar engaged users in a design conversation as it visited homes, studios, gigs, workshops and lessons, and how this revealed the diversity and utility of its digital record. We describe how this record was captured and flexibly mapped to the physical guitar and proxy artefacts. We contribute a conceptual framework for accountable artefacts that articulates how multiple and complex mappings between physical artefacts and their digital records may be created, appropriated, shared and interrogated to deliver accounts of provenance and use as well as methodological reflections on technology probes.

Fresh and local: the rural produce market as a site for co-design, ubiquitous technological intervention and digital-economic development

Ethnographic studies have played a key part in informing the design and development of a multitude of ubiquitous systems, from control room systems to pervasive games. While other papers have often focused on systems developed for urban contexts, this paper presents the initial findings of a study that focuses on a rural produce market in West Wales as a site for ubiquitous multimedia system-based intervention, digital economic considerations and co-design. The findings relate to the initial ethnographic fieldwork, digital-economic considerations for the site, the evolution of a participatory design strategy for developing a Market Portal and - importantly -- the way that these are informing the design of the ubiquitous technologies relating to the Market Portal.

Supporting novel home network management interfaces with openflow and NOX

The Homework project has examined redesign of existing home network infrastructures to better support the needs and requirements of actual home users. Integrating results from several ethnographic studies, we have designed and built a home networking platform providing detailed per-flow measurement and management capabilities supporting several novel management interfaces. This demo specifically shows these new visualization and control interfaces (1), and describes the broader benefits of taking an integrated view of the networking infrastructure, realised through our routers augmented measurement and control APIs (2). Aspects of this work have been published: the Homework Database in Internet Management (IM) 2011 [3] and implications of the ethnographic results are to appear at the SIGCOMM W-MUST workshop 2011 [2]. Separate, more detailed expositions of the interface elements and system performance and implications are currently under submission at other venues. A partial code release is already available and we anticipate fuller public beta release by Q4 2011.