Don Cruickshank

myExperiment: a repository and social network for the sharing of bioinformatics workflows

myExperiment (http://www.myexperiment.org) is an online research environment that supports the social sharing of bioinformatics workflows. These workflows are procedures consisting of a series of computational tasks using web services, which may be performed on data from its retrieval, integration and analysis, to the visualization of the results. As a public repository of workflows, myExperiment allows anybody to discover those that are relevant to their research, which can then be reused and repurposed to their specific requirements. Conversely, developers can submit their workflows to myExperiment and enable them to be shared in a secure manner. Since its release in 2007, myExperiment currently has over 3500 registered users and contains more than 1000 workflows. The social aspect to the sharing of these workflows is facilitated by registered users forming virtual communities bound together by a common interest or research project. Contributors of workflows can build their reputation within these communities by receiving feedback and credit from individuals who reuse their work. Further documentation about myExperiment including its REST web service is available from http://wiki.myexperiment.org. Feedback and requests for support can be sent to bugs@myexperiment.org.

Why Linked Data is Not Enough for Scientists

Scientific data stands to represent a significant portion of the linked open data cloud and science itself stands to benefit from the data fusion capability that this will afford. However, simply publishing linked data into the cloud does not necessarily meet the requirements of reuse. Publishing has requirements of provenance, quality, credit, attribution, methods in order to provide the \emph{reproducibility} that allows validation of results. In this paper we make the case for a scientific data publication model on top of linked data and introduce the notion of \emph{Research Objects} as first class citizens for sharing and publishing.

myExperiment: Defining the Social Virtual Research Environment

The myExperiment virtual research environment supports the sharing of research objects used by scientists, such as scientific workflows. For researchers it is both a social infrastructure that encourages sharing and a platform for conducting research, through familiar user interfaces. For developers it provides an open, extensible and participative environment. We describe the design, implementation and deployment of myExperiment and suggest that its four capabilities - research objects, social model, open environment and actioning research - are necessary characteristics of an effective Virtual Research Environment for e-research and open science.

The literacy fieldtrip: using UbiComp to support children's creative writing

Fieldtrips, traditionally associated with science, history and geography teaching, have long been used to support childrens learning by allowing them to engage with environments first-hand. Recently, ubiquitous computing (UbiComp) has been used to enhance fieldtrips in these educational areas by augmenting environments with a range of instruments, devices and sensors. However, the sorts of interaction design that UbiComp makes possible have the potential not just to enhance the value of educational techniques in known application areas, but also to expand the application of those techniques into new areas of curriculum. We report on a UbiComp-supported fieldtrip to support creative writing, associated with the learning of literacy skills. We discuss how the fieldtrip, designed and run in the grounds of a historic English country house with Year 5 UK schoolchildren, engendered interactions which changed both the processes and products of creative writing, with benefits for both teachers and children.

Requirements for in-situ authoring of location based experiences

In this paper we describe an investigation into the requirements for and the use of in-situ authoring in the creation of location based pervasive and UbiComp experiences. We will focus on the co-design process with users that resulted in a novel visitor experience to a historic country estate. This has informed the design of new, in-situ, authoring tools supplemented with tools for retrospective revisiting and reorganization of content. An initial trial of these new tools will be discussed and conclusions drawn as to the appropriateness of such tools. Further enhancements as part of future trials will also be described.

Unfolding understandings: co-designing UbiComp In Situ , over time

A key challenge in co-designing UbiComp is that users may have limited understanding or experience of these technologies. While the value of situated co-design activities for promoting understanding is known, the role of time is less well researched. Here we describe and reflect on a range of co-design activities carried out with the curators of an historic English manor house to create novel visitor tours. We show how an ensemble of situated co-design activities over time led to the unfolding of user understanding around issues of content, technology and user experience, in turn leading to a progressive re-imagining of practice. This points to the importance of time and variety of in-situ activities to help people engage as co-designers in creating novel UbiComp-enabled experiences.

Its about time: link streams as continuous metadata

As enabling technologies become available there is an increasing use of temporal media streams, such as audio and video, within a hypertext context. In this paper we present the rationale and requirements for delivering continuous metadata alongside the media stream, and focus on linking as our case study. We consider the mechanism for delivery of the metadata across a distributed system, the format and content of the metadata flow itself, and the presentation of the media and augmenting metadata to the user. Two initial proof of concept applications have been developed to demonstrate these concepts, which we describe. Finally we propose a framework for highly distributed delivery and processing of multicast continuous metadata, as a part of the infrastructure necessary to provide a more complete multimedia environment for hypermedia systems.

The Evolution of myExperiment

The myExperiment social website for sharing scientific workflows, designed according to Web 2.0 principles, has grown to be the largest public repository of its kind. It is distinctive for its focus on sharing methods, its researcher-centric design and its facility to aggregate content into sharable ‘research objects’. This evolution of myExperiment has occurred hand in hand with its users. myExperiment now supports Linked Data as a step toward our vision of the future research environment, which we categorise here as 3rd generation e-Research.

Opening new gateways to workflows for life scientists

The combination of highly complex biology problems and varying IT skills among life scientists poses a unique challenge in designing bioinformatics programs. The set of tools and initiatives described in this work shows new ways of making life science workflows more accessible to the community. Our aim is to help bioinformaticians help biologists. We present how to make Taverna workflows available from within Galaxy, both widely used bioinformatics platforms. Calling Galaxy tools from Taverna is also discussed. In addition, we describe a web application that allows a user to run arbitrary Taverna workflows by only using a web browser.

Architectural design of a multi-agent system for handling metadata streams

We have designed a multi-agent architecture to deliver metadata streams synchronously with multimedia streams over a wide-area network. To this end, we have devised a simple protocol for synchronising agents to a media clock. This protocol defines the concept of a deadline, after which servers can drop data because it can no longer reach clients in time. We also introduce a new concept of a contract as a first-class entity representing a successful subscription; a contract is used by agents as a session identifier during the navigation of streams. Quality of service is a vital element of this architecture because of the need to deliver metadata on time. As a result, our architecture supports various communication protocols, including \udp, \rmi, \ssl, or multicast. This resulted in a return to a more declarative form of speech acts, totally orthogonal to a notion of virtual communication channel used to manage the quality of service of communication.