Although the benefits of teleoperation are well known, the current implementations require high levels of skill which exclude the average user. One of the difficulties is the delay between sending a command and the movement of the robot which can impact an operator’s ability to safely, and effectively perform tasks. Furthermore, the rejection of commands due to unattainable goals (e.g. outside the robot’s joint limits) can leave the operator confused and frustrated. Advancements in research, such as the use of virtual reality (VR) and inverse kinematic techniques are steadily making robot control more feasible for everyday users, but there is still a lack of understanding of what the robot can or cannot do based on its limits and environment. A benefit of VR over other display methods is the ability to customise the immersive environment that the robot is in. In this paper we take advantage of that benefit to create three visual feedback techniques which give the user information on their commands. A user study was conducted comparing our techniques. The results show that higher levels of visual feedback result in quicker task completion times, lower mental workload and a better user experience.

Abstract Digital replication of woven fabrics presents significant challenges across a variety of sectors, from online retail to entertainment industries. To address this, we introduce an inverse rendering pipeline designed to estimate pattern, geometry, and appearance parameters of woven fabrics given a single close‐up image as input. Our work is capable of simultaneously optimizing both discrete and continuous parameters without manual interventions. It outputs a wide array of parameters, encompassing discrete elements like weave patterns, ply and fiber number, using Simulated Annealing. It also recovers continuous parameters such as reflection and transmission components, aligning them with the target appearance through differentiable rendering. For irregularities caused by deformation and flyaways, we use 2D Gaussians to approximate them as a post‐processing step. Our work does not pursue perfect matching of all fine details, it targets an automatic and end‐to‐end reconstruction pipeline that is robust to slight camera rotations and room light conditions within an acceptable time (15 minutes on CPU), unlike previous works which are either expensive, require manual intervention, assume given pattern, geometry or appearance, or strictly control camera and light conditions.

In the teleoperation of robots, the absence of proprioception means that visual information plays a crucial role. Previous research has investigated methods to offer optimal vantage points to operators during teleoperation, with virtual reality (VR) being proposed as a mechanism to give the operator intuitive control over the viewpoint for improved visibility and interaction. However, the most effective perspective for robot operation and the optimal portrayal of the robot within the virtual environment remain unclear. This paper examines the impact of various visual conditions on users’ efficiency and preference in controlling a simulated robot via VR. We present a user study that compares two operating perspectives and three robot appearances. The findings indicate mixed user preferences and highlight distinct advantages associated with each perspective and appearance combination. We conclude with recommendations on selecting the most beneficial perspective and appearance based on specific application requirements.

The demands of creating an immersive Virtual Reality (VR) experience often exceed the raw capabilities of graphics hardware. Perceptually-driven techniques can reduce rendering costs by directing effort away from features that do not significantly impact the overall user experience while maintaining a high level of quality where it matters most. One such approach is foveated rendering, which allows for a reduction in the quality of the image in the peripheral region of the field-of-view where lower visual acuity results in users being less able to resolve fine details. 6 Degrees of Freedom tracking allows for the exploration of VR environments through different modalities, such as user-generated head or body movements. The effect of self-induced motion on rendering optimization has generally been overlooked and is not yet well understood. To explore this, we used Variable Rate Shading (VRS) to create a foveated rendering method triggered by the translational velocity of the users and studied different levels of shading Level-of-Detail (LOD). We asked 10 participants in a within-subjects design to report whether they noticed a degradation in the rendering of a rich environment when performing active ego-movement or when being passively transported through the environment. We ran a psychophysical experiment using an accelerated stochastic approximation staircase method and modified the diameter and the LOD of the peripheral region. Our results show that self-induced walking can be used to significantly improve the savings of foveated rendering by allowing for an increased size of the low-quality area in a foveated algorithm compared to the passive condition. After fitting psychometric functions showcasing the percentage of correct responses related to different shading rates in the two types of movements, we also report the threshold severity (75%) point for when participants are able to detect such degradation. We argue such metrics can inform the future design of movement-dependent foveated techniques that could reduce computational load and increase energy savings.

Commercialisation of augmented reality (AR) devices has led to their growing application in domestic environments and leisure activities. One such domain is that of television, where AR is one of several technologies driving innovation (c.f. Internet broadcasting, second screen devices). We conduct a systematic literature review to quantify research at the intersection of AR and broadcast television. We identify six common themes and a set of cross-cutting design decisions. We distill this information into a design space incorporating six dimensions: abstraction, interaction, time, display, context and editorial control. We provide methods to operationalise the dimensions to enable research and development of novel concepts, and through this generate six design guidelines to shape future activity at the intersection of AR and television.

When are two entries about a small molecule in different datasets the same? If they have the same drug name, chemical structure, or some other criteria? The choice depends upon the application to which the data will be put. However, existing Linked Data approaches provide a single global view over the data with no way of varying the notion of equivalence to be applied.In this paper, we present an approach to enable applications to choose the equivalence criteria to apply between datasets. Thus, supporting multiple dynamic views over the Linked Data. For chemical data, we show that multiple sets of links can be automatically generated according to different equivalence criteria and published with semantic descriptions capturing their context and interpretation. This approach has been applied within a large scale public-private data integration platform for drug discovery. To cater for different use cases, the platform allows the application of different lenses which vary the equivalence rules to be applied based on the context and interpretation of the links.

PDFX is a rule-based system designed to reconstruct the logical structure of scholarly articles in PDF form, regardless of their formatting style. The system's output is an XML document that describes the input article's logical structure in terms of title, sections, tables, references, etc. and also links it to geometrical typesetting markers in the original PDF, such as paragraph and column breaks. The key aspect of the presented approach is that the rule set used relies on relative parameters derived from font and layout specifics of each article, rather than on a template-matching paradigm. The system thus obviates the need for domain- or layout-specific tuning or prior training, exploiting only typographical conventions inherent in scientific literature. Evaluated against a significantly varied corpus of articles from nearly 2000 different journals, PDFX gives a 77.45 F1 measure for top-level heading identification and 74.03 for extracting individual bibliographic items. The service is freely available for use at http://pdfx.cs.man.ac.uk/.

MOTIVATION: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. RESULTS: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations. AVAILABILITY: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl. CONTACT: [email protected].

Nonlinear forms of diagrammatic presentation, such as node-arc graphs, are a powerful and elegant means of visual information presentation. Although providing nonvisual access is now routine for many forms of linear information, it becomes more difficult as the structure of the information becomes increasingly nonlinear. An understanding of the ways in which graphs benefit sighted people, based on experiments and the literature, together with the difficulties encountered when exploring graphs nonvisually, helps form a solution for nonvisual access to graphs. This article proposes that differing types of annotation offer a powerful and flexible technique for transferring the benefits of graph-based diagrams, as well as for reducing disorientation while moving around the graph and for tackling some of the inherent disadvantages of using sound. Different forms of annotation that may address these problems are explored, classified, and evaluated, including notes designed to summarise and to aid node differentiation. Graph annotation may be performed automatically, creating a graph that evaluation shows requires less mental effort to explore and on which tasks can be achieved more effectively and more efficiently.

BACKGROUND: With the continued growth in the volume both of experimental G protein-coupled receptor (GPCR) data and of the related peer-reviewed literature, the ability of GPCR researchers to keep up-to-date is becoming increasingly curtailed. RESULTS: We present work that integrates the biological data and annotations in the GPCR information system (GPCRDB) with next-generation methods for intelligently exploring, visualising and interacting with the scientific articles used to disseminate them. This solution automatically retrieves relevant information from GPCRDB and displays it both within and as an adjunct to an article. CONCLUSIONS: This approach allows researchers to extract more knowledge more swiftly from literature. Importantly, it allows reinterpretation of data in articles published before GPCR structure data became widely available, thereby rescuing these valuable data from long-dormant sources.

Computational and data-intensive science increasingly depends on a large Web Service infrastructure, as services that provide a broad array of functionality can be composed into workflows to address complex research questions. In this context, the goal of service registries is to offer accurate search and discovery functions to scientists. Their effectiveness, however, depends not only on the model chosen to annotate the services, but also on the level of abstraction chosen for the annotations. The work presented in this paper stems from the observation that current annotation models force users to think in terms of service interfaces, rather than of high-level functionality, thus reducing their effectiveness. To alleviate this problem,we introduce Functional Units (FU) as the elementary units of information used to describe a service. Using popular examples of services for the Life Sciences, we define FUs as configurations and compositions of underlying service operations, and show how functional-style service annotations can be easily realised using the OWL semantic Web language. Finally, we suggest techniques for automating the service annotations process, by analysing collections of workflows that use those services.

MOTIVATION: In recent years, the gulf between the mass of accumulating-research data and the massive literature describing and analyzing those data has widened. The need for intelligent tools to bridge this gap, to rescue the knowledge being systematically isolated in literature and data silos, is now widely acknowledged. RESULTS: To this end, we have developed Utopia Documents, a novel PDF reader that semantically integrates visualization and data-analysis tools with published research articles. In a successful pilot with editors of the Biochemical Journal (BJ), the system has been used to transform static document features into objects that can be linked, annotated, visualized and analyzed interactively (http://www.biochemj.org/bj/424/3/). Utopia Documents is now used routinely by BJ editors to mark up article content prior to publication. Recent additions include integration of various text-mining and biodatabase plugins, demonstrating the system's ability to seamlessly integrate on-line content with PDF articles. AVAILABILITY: http://getutopia.com.

MOTIVATION: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. RESULTS: BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web. AVAILABILITY: The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community.

Abstract Summary: Arcadia translates text-based descriptions of biological networks (SBML files) into standardized diagrams (SBGN PD maps). Users can view the same model from different perspectives and easily alter the layout to emulate traditional textbook representations. Availability and Implementation: Arcadia is written in C++. The source code is available (along with Mac OS and Windows binaries) under the GPL from http://arcadiapathways.sourceforge.net/ Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

SUMMARY: The EMBRACE Registry is a web portal that collects and monitors web services according to test scripts provided by the their administrators. Users are able to search for, rank and annotate services, enabling them to select the most appropriate working service for inclusion in their bioinformatics analysis tasks. AVAILABILITY AND IMPLEMENTATION: Web site implemented with PHP, Python, MySQL and Apache, with all major browsers supported. (www.embraceregistry.net).

MOTIVATION: In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held remotely on the internet or locally on in-house servers. Supporting these tasks are ad hoc collections of data-manipulation tools, scripting languages and visualisation software, which are often combined in arcane ways to create cumbersome systems that have been customized for a particular purpose, and are consequently not readily adaptable to other uses. For many day-to-day bioinformatics tasks, the sizes of current databases, and the scale of the analyses necessary, now demand increasing levels of automation; nevertheless, the unique experience and intuition of human researchers is still required to interpret the end results in any meaningful biological way. Putting humans in the loop requires tools to support real-time interaction with these vast and complex data-sets. Numerous tools do exist for this purpose, but many do not have optimal interfaces, most are effectively isolated from other tools and databases owing to incompatible data formats, and many have limited real-time performance when applied to realistically large data-sets: much of the user's cognitive capacity is therefore focused on controlling the software and manipulating esoteric file formats rather than on performing the research. METHODS: To confront these issues, harnessing expertise in human-computer interaction (HCI), high-performance rendering and distributed systems, and guided by bioinformaticians and end-user biologists, we are building reusable software components that, together, create a toolkit that is both architecturally sound from a computing point of view, and addresses both user and developer requirements. Key to the system's usability is its direct exploitation of semantics, which, crucially, gives individual components knowledge of their own functionality and allows them to interoperate seamlessly, removing many of the existing barriers and bottlenecks from standard bioinformatics tasks. RESULTS: The toolkit, named Utopia, is freely available from http://utopia.cs.man.ac.uk/.

Programmatic access to data and tools through the web using so-called web services has an important role to play in bioinformatics. In this article, we discuss the most popular approaches based on SOAP/WS-I and REST and describe our, a cross section of the community, experiences with providing and using web services in the context of biological sequence analysis. We briefly review main technological approaches as well as best practice hints that are useful for both users and developers. Finally, syntactic and semantic data integration issues with multiple web services are discussed.

Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as "thought in cold storage," and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.

Abstract Many scientific phenomena in large high‐resolution datasets such as the U.K. Ocean Circulation and Advanced Modelling (OCCAM) ocean model are better discovered through visualization than by algorithmic analysis: it is often more straightforward to see a feature than it is to characterize it numerically. Using traditional rendering techniques, the size of modern datasets presents a challenge for even high‐end graphical supercomputers, and the cost of such hardware limits its availability for day‐to‐day analysis. We present an architecture that brings visual analysis to the desktop by exploiting consumer‐grade graphics hardware in order to provide initial interactive exploration and Web services to enable finer‐grained analysis and interoperability with traditional visualization tools. Copyright © 2006 John Wiley & Sons, Ltd.

Network architectures for collaborative virtual reality have traditionally been dominated by client-server and peer-to-peer approaches, with peer-to-peer strategies typically being favored where minimizing latency is a priority, and client-server where consistency is key. With increasingly sophisticated behavior models and the demand for better support for haptics, we argue that neither approach provides sufficient support for these scenarios and, thus, a hybrid architecture is required. We discuss the relative performance of different distribution strategies in the face of real network conditions and illustrate the problems they face. Finally, we present an architecture that successfully meets many of these challenges and demonstrate its use in a distributed virtual prototyping application which supports simultaneous collaboration for assembly, maintenance, and training applications utilizing haptics.

This paper describes the evaluation of software, software designed to allow visually impaired users to explore the structures of chemical molecules using a speech based presentation. Molecular structures are typically presented as two dimensional schematics, and are an important example of a widely used form of diagram -- the graph. software is designed for exploring this specific class of graph. Among its features is the ability to recognise and make explicit features of the graph that would otherwise need to be inferred. The evaluation compared software with a simpler version without this facility, and found that participants were able to explore molecular structures more easily. We discuss the software, evaluation and results, particularly comparing them with theoretical considerations about how sighted readers use diagrams. Finally, we extract the important issues for non-visual graph presentation: making implicit features explicit; enabling hierarchical and connection-based browsing; allowing annotation; and helping users keep their orientation.

One aspect of non-visual visualisation is providing accessibility to diagrams for users with visual impairments. In this paper, we review the literature on diagrams and non-visual presentation in order to elucidate the issues involved in making graph based diagrams accessible using speech and non-speech sound. First we examine the nature, scope and uses of these diagrams. We then describe the nature of diagrams: how do diagrams differ from other representations; how do sighted readers read, understand, and extract information from diagrams; what cognitive processes do diagrams facilitate; and what factors affect how diagrams may be understood? After a comparison of visual with aural presentation we discuss the work presented by others in this field, particularly looking at their reasons for implementing how they do in light of our examination of visual comprehension. The paper concludes with a discussion of how these issues combine and conflict to influence requirements for interface design.

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.

Physically-based modelling is a powerful technique for specifying the laws and characteristics of virtual environments (VEs) and the objects they contain. In this paper, we describe Iota, a component framework for creating and interacting with multi-body physically-based models in VEs. In conclusion, we present two case studies implemented within the framework.

Virtual environments present opportunities for novel interaction with and visualisation of abstract data. However, the inherent difficulties of rendering 3D environments, as well as bottlenecks in traditional virtual reality systems, make real-time manipulation of realistic amounts of data difficult. We present QSPACE, a data visualisation tool with which we have begun to explore techniques and architectures for making real-time interaction with largest amounts of data possible.

The need for a real-world driving problem to guide technology development has long been recognised. However, this does not guarantee the identification of requirements for technology development. This paper argues that a more systematic approach is needed for choosing and making best use of a driving problem for CVE technology. The method consists of identifying the stakeholders in the technology development project. A series of issues must then be addressed: choice of problem area, choice of application, choice of research approach, design of the application, ensuring use by real users, choice of method of study, and identification of technology requirements. The method is illustrated by considering the development of the Deva CVE system with an art-based application and with an educational application.

In this paper we present work undertaken by the Advanced Interfaces Group at the University of Manchester on the design and development of a system to support large numbers of geographically distributed users in complex, large-scale virtual environments (VEs).We shown how the problem of synchronisation in the face of network limitations is being addressed by the Deva system through the exploitation of subjectivity. Further, we present a model for flexibly describing object behaviours in the VEs.Applications of the system in use are described.

No abstract available.

This paper describes a publicly available virtual reality (VR) system, GNU/MAVERIK, which forms one component of a complete 'VR operating system'. We give an overview of the architecture of MAVERIK, and show how it is designed to use application data in an intelligent way, via a simple, yet powerful, callback mechanism which supports an object-oriented framework of classes, objects and methods. Examples are given which illustrate different uses of the system, and typical performance levels.

Lag in network technology prevents absolute synchronization of distributed Virtual Environments (VEs); our experience of them is in this sense inherently subjective. We describe how subjectivity of this kind provides a means of enabling coherent shared experience in a VE, and present an architecture based on this.