Colin Leonard Bird

Automating the linking of content and concept

In previous work we have described a multimedia system, MAVIS 2, supporting content and concept based retrieval and navigation. A central component of the system is a multimedia thesaurus in which media content is associated with appropriate concepts in a semantic layer. A major challenge is identifying and constructing these associations in a particular application without requiring a huge amount of manual effort. In this paper we propose a two phase approach to the problem. In the first phase, latent semantic analysis is used to associate metadata available for some media objects with concept class descriptions. This facilitate automatic associations to be made with the concept layer of the those media objects. In the second phase, media content matching is used to classify media objects without metadata through their similarity to media objects classified in phase 1.

Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance

Cheminformatics is evolving from being a field of study associated primarily with drug discovery into a discipline that embraces the distribution, management, access, and sharing of chemical data. The relationship with the related subject of bioinformatics is becoming stronger and better defined, owing to the influence of Semantic Web technologies, which enable researchers to integrate heterogeneous sources of chemical, biochemical, biological, and medical information. These developments depend on a range of factors: the principles of chemical identifiers and their role in relationships between chemical and biological entities; the importance of preserving provenance and properly curated metadata; and an understanding of the contribution that the Semantic Web can make at all stages of the research lifecycle. The movements toward open access, open source, and open collaboration all contribute to progress toward the goals of integration.

First steps towards semantic descriptions of electronic laboratory notebook records

In order to exploit the vast body of currently inaccessible chemical information held in Electronic Laboratory Notebooks (ELNs) it is necessary not only to make it available but also to develop protocols for discovery, access and ultimately automatic processing. An aim of the Dial-a-Molecule Grand Challenge Network is to be able to draw on the body of accumulated chemical knowledge in order to predict or optimize the outcome of reactions. Accordingly the Network drew up a working group comprising informaticians, software developers and stakeholders from industry and academia to develop protocols and mechanisms to access and process ELN records. The work presented here constitutes the first stage of this process by proposing a tiered metadata system of knowledge, information and processing where each in turn addresses a) discovery, indexing and citation b) context and access to additional information and c) content access and manipulation. A compact set of metadata terms, called the elnItemManifest, has been derived and caters for the knowledge layer of this model. The elnItemManifest has been encoded as an XML schema and some use cases are presented to demonstrate the potential of this approach.

Web-based services for drug design and discovery

Introduction: Reviews of the development of drug discovery through the 20th century recognised the importance of chemistry and increasingly bioinformatics, but had relatively little to say about the importance of computing and networked computing in particular. However, the design and discovery of new drugs is arguably the most significant single application of bioinformatics and cheminformatics to have benefitted from the increases in the range and power of the computational techniques since the emergence of the World Wide Web, commonly now referred to as simply ‘the Web’. Web services have enabled researchers to access shared resources and to deploy standardized calculations in their search for new drugs. Areas covered: This article first considers the fundamental principles of Web services and workflows, and then explores the facilities and resources that have evolved to meet the specific needs of chem- and bio-informatics. This strategy leads to a more detailed examination of the basic components that characterise molecules and the essential predictive techniques, followed by a discussion of the emerging networked services that transcend the basic provisions, and the growing trend towards embracing modern techniques, in particular the Semantic Web. Expert opinion: In the opinion of the authors, the issues that require community action are: increasing the amount of chemical data available for open access; validating the data as provided; and developing more efficient links between the worlds of cheminformatics and bioinformatics. The goal is to create ever better drug design services.

ChemTrove: Enabling a Generic ELN To Support Chemistry through the Use of Transferable Plug-ins and Online Data Sources

In designing an Electronic Lab Notebook (ELN), there is a balance to be struck between keeping it as general and multidisciplinary as possible for simplicity of use and maintenance and introducing more domain-specific functionality to increase its appeal to target research areas. Here, we describe the results of a collaboration between the Royal Society of Chemistry (RSC) and the University of Southampton, guided by the aims of the Dial-a-Molecule Grand Challenge, intended to achieve the best of both worlds and augment a discipline-agnostic ELN, LabTrove, with chemistry-specific functionality and using data provided by the ChemSpider platform. This has been done using plug-in technology to ensure maximum transferability with minimal effort of the chemistry functionality to other ELNs and equally other subject-specific functionality to LabTrove. The resulting product, ChemTrove, has undergone a usability trial by selected academics, and the resulting feedback will guide the future development of the underlying ELN technology.

Speed considerations for electrochromic displays

The elect rochromic effect based on the reversible electro-deposition of a viologen radical cation has been applied to information display systems. Problems of multiplexing can be overcome by the use of an auxiliary switch, such as a thin-film transistor. The question of speed is the subject of this paper, which discusses the factors influencing the contrast ratio of an electrochromic display. The contrast ratio is determined by electrochemical and optical considerations, the former governing the amount of material deposited and the latter the visual effect of the deposit. Electrochemically, the deposition may be influenced by a variety of mechanisms, including diffusion, migration, electrode kinetics and deposit resistance. Multiple pulse driving gives increased speed in diffusion-limited cases. Optically, the perceived contrast is maximised by increasing the absorbance of the deposited material and by optimising the diffuse reflectance of the display electrode.

An XML-based approach to automated software testing

The advantages of automating the functional testing of application software are well-known, but the manner of automation can lead to difficulties in authenticating the test coverage. In this paper we consider the class of automated tests in which a driver tool simulates the input and responses of a human operator and sequentially checks the output generated by the application software. The driver tool commonly employs its own language to describe the tasks it can be required to perform, for example:• Issue a sequence of characters that simulate input from the keyboard.• Verify that a segment of the display buffer contains the expected bit pattern.Although these tasks are simply stated, the language to effect them in a test script can become complex and hard to maintain. Furthermore, reading the driver tool program is not an effective way to confirm that the test script performs its tasks to the test specification.XML (eXtensible Markup Language)[1)] scripts offer a rigorous intermediate description that can be readily translated into both the driver tool test script and a readable statement of the task the test performs. The advantages accruing from the use of XML are:• The XML scripts are easy to edit, simplifying basic script maintenance. New steps can be included for testing bug fixes.• Content review becomes much easier, as the relevant aspects of the script can be rendered in a readily readable form, such as HTML;• Global changes become feasible, as the structured nature of XML documents makes it possible to search for specific element content;• The structure of the XML document can itself be checked, for example using a validating editor such as Xeena [2)].In the next section we describe an example of automated testing using a driver tool, based on XML scripts. The application being tested is called Wired for Learning [3)] and provides the IT infrastructure for schools to:• Enhance communication between teachers, students and parents.• Enable teachers to plan and share ideas for lessons and activities, linking in with national standards.• Organize team projects involving teachers and students across classes and schools, with the option of inviting members of the community to provide additional information.• Provide an events calendar to keep everyone up to date with what is happening in the school.• Allow teachers easily to create their own home pages for information dissemination.

Human Aspects of Smart Spaces for Knowledge Transfer

During May and June 2011, we ran two workshops with a theme entitled “Smart Spaces for Smart People” [1]. Although organized under the auspices of the e-Science Institute, the participants came from a variety of disciplines and brought a range interests. The workshops themselves were run as experiments in running smart meetings with the intentions of exchanging and recording knowledge and decisions discussed in the meeting. A recurring theme in the workshops was not only that technology can be provided in a smart space to help in the knowledge transfer and recording process, but also that the technology will only be adopted and exploited if the users of the smart space can easily use it. There are other human factors that affect the success of collaboration in a smart space. These include the willingness for participates to collaborate if they have concerns over privacy and anonymity, particularly when discussions and decisions are recorded using technology. The dynamics of how participants work together in groups to transfer knowledge can also be enhanced through the use of smart spaces. The fact that the workshops were run in different physical environments also provided insights into how the physical design of the meeting space might have on effective collaboration and therefore effective transmission of knowledge. This paper is the second in a series of three, each dealing with different aspects of the workshops and how they influenced our thinking about knowledge transfer meetings, particularly in the context of sharing research outputs.

Smart Meetings: Experimenting with Space

During May and June 2011, motivated by the need to improve techniques for recording the processes and outputs of research, we ran two workshops under the auspices of the e-Science Institute. The theme title was “Smart Spaces for Smart People”. Although our initial intention was to explore interactions between the physical and digital worlds, the emphasis changed to the productive exploitation of spaces ascribed as smart. We explored the quality of smartness in the context of smart meetings, which led us to conclude that the role of hardware and software technologies is to confer capability. For a system to achieve smartness, we deem certain components to be essential, most notably people. However, we also consider the role of both technological and traditional techniques for capturing meeting outcomes. We learned lessons that are applicable not only to meetings about research but also in the more general knowledge transfer context. We conclude that the way forward for exploiting smart spaces relies on design and on empowering the users of such spaces in that design. This paper is the first in a series of three, each dealing with different aspects of the workshops and how they influenced our thinking about knowledge transfer meetings, particularly in the context of sharing research outputs.

Scientific and technical data sharing: a trading perspective

It is arguably a precept that the open sharing of data maximises the scientific utility of the research that generated that data. Indeed, progress depends on individual scientists being able to build on the results produced by others. The means to facilitate sharing undoubtedly exist, but various studies have identified reluctance among researchers to share information with their peers, at least until the professional priorities of the original researchers have been accommodated. With a view to encouraging less inhibited collaboration, we appraise the processes of data exchange from the perspective of a trading environment and consider how data exchanges might promote (or perhaps hinder) collaboration in data-rich scientific research disciplines and how such an exchange might be set up. We suggest an exchange with trusted brokers (akin to the commodity markets) as a way to overcome the challenges of the current environment. We conclude by encouraging the scientific and technical community to debate the merits of a trading perspective on data sharing and exchange.