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Background In about one in 10,000 cases, a published article is retracted. This very often means that the results it reports are flawed. Several authors have voiced concerns about the presence of retracted research in the memory of science. In particular, a retracted result is propagated by citing it. In the published literature, many instances are given of retracted articles that are cited both before and after their retraction. Even worse is the possibility that these articles in turn are cited in such a way that the retracted result is propagated further. Methods We have conducted a case study to find out how a retracted article is cited and whether retracted results are propagated through indirect citations. We have constructed the entire citation network for this case. Results We show that directly citing articles is an important source of propagation of retracted research results. In contrast, in our case study, indirect citations do not contribute to the propagation of the retracted result. Conclusions While admitting the limitations of a study involving a single case, we think there are reasons for the non-contribution of indirect citations that hold beyond our case study. Electronic supplementary material The online version of this article (doi:10.1186/s41073-016-0008-5) contains supplementary material, which is available to authorized users.

Balance input in human-computer interfaces can be beneficial, enjoyable and entertaining. Users can navigate a virtual (game) world or an (empirical) dataset while having their hands free to issue other commands. A new low-cost balance interface, the Nintendo balance board, offers more widespread use of this form of input. We performed two experiments that explore the fun and efficiency of this interface for navigating simple virtual worlds. In our first study, we compared the Nintendo balance board to a hand-held Wiimote for navigating a 2D maze and found that users completed this task slower with the balance board. However, the balance board was considered more intuitive, easy to learn and `much fun'. In a follow-up study, we compared two navigation methods based on shifting the center of body mass on the balance board using a Fitts' law evaluation. We found that although both methods are outperformed by a standard mouse and a self-centering joystick, they are enjoyed more than these more traditional interfaces. However, the board interfaces performed similarly for easier navigation tasks; leaving the hands free for manipulation tasks while coarse navigation can be performed by the shifting body mass

Background Computational support is essential in order to reason on the dynamics of biological systems. We have developed the software tool ANIMO (Analysis of Networks with Interactive MOdeling) to provide such computational support and allow insight into the complex networks of signaling events occurring in living cells. ANIMO makes use of timed automata as an underlying model, thereby enabling analysis techniques from computer science like model checking. Biology experts are able to use ANIMO via a user interface specifically tailored for biological applications. In this paper we compare the use of ANIMO with some established formalisms on two case studies. Results ANIMO is a powerful and user-friendly tool that can compete with existing continuous and discrete paradigms. We show this by presenting ANIMO models for two case studies: Drosophila melanogaster circadian clock, and signal transduction events downstream of TNF α and EGF in HT-29 human colon carcinoma cells. The models were originally developed with ODEs and fuzzy logic, respectively. Conclusions Two biological case studies that have been modeled with respectively ODE and fuzzy logic models can be conveniently modeled using ANIMO. The ANIMO models require less parameters than ODEs and are more precise than fuzzy logic. For this reason we position the modelling paradigm of ANIMO between ODEs and fuzzy logic. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0286-z) contains supplementary material, which is available to authorized users.

Probabilistic approaches for data integration have much potential [7]. We view data integration as an iterative process where data understanding gradually increases as the data scientist continuously refines his view on how to deal with learned intricacies like data conflicts. This paper presents a probabilistic approach for integrating data on groupings. We focus on a bio-informatics use case concerning homology. A bio-informatician has a large number of homology data sources to choose from. To enable querying combined knowledge contained in these sources, they need to be integrated. We validate our approach by integrating three real-world biological databases on homology in three iterations.

On information markets, many suppliers and buyers of information goods exchange values. Some of these goods are data, whose value is created in buyer interactions with data sources. These interactions are enabled by data market services (DMS). DMS give access to one or several data sources. The major problems with the creation of information value in these contexts are (1) the quality of information retrievals and related queries, and (2) the complexity of matching information needs and supplies when different semantics are used by source systems and information buyers. This study reports about a prototype DMS (called CIRBA), which employs an ontology-based information retrieval system to solve semantic problems for a DMS. the DMS quality is tested in an experiment to assess its quality from a user perspective against a traditional data warehouse (with SQL) solution. The CIRBA solution gave substantially higher user satisfaction than the data warehouse alternative.Keywords: data market services, data warehouse, information retrieval, ontology

The economic impact of information and communication technology (ICT) on the academic library and on the academic institution are discussed in terms of changes in the value chain of scientific information induced by the use of ICT. Argues that ICT is a very strong engine for change as it has the potential not only to transform the research information system, but also the educational information system or even the education system at large. Academic institutions will have to create their own publishing and archiving environments using the same technology as in research publishing. These developments will have a profound impact on the value chain of scientific information as it leads academic institutions to assume entirely new roles in this chain and to develop new capabilities. As well as a digital collection strategy, academic libraries will develop strategies for supporting e‐learning and e‐publishing. This leads to changes in the economic conditions at the institutional and also industrial level. The developments will be discussed in general.

Changes in the value chain induced by the use of information and communication technology (ICT) are discussed. ICT will lead to innovation not only in the research information system but also in the educational information system or even in the education system at large. Widespread use of ICT allows universities to change from supply-push to demandpull education. Universities will create their own publishing and archiving environments.

Anderungen in der Wertschopfungskette werden diskutiert, insbesondere Anderungen in dieser Wertschopfungskette, die durch die Benutzung von Informations- und Kommunikationstechnologie (IT) entstehen. IT hat einen so grosen Einfluss auf die Entwicklung, weil sie das Potenzial nicht nur zur innovativen Veranderung des Forschungsinformationssystems sondern auch des Erziehungs- und Ausbildungsinformationssystems, ja des gesamten Erziehungs- und Ausbildungssystems hat. Eine Voraussetzung fur diese Entwicklung ist, dass die Hochschulen eine eigene Publikations- und Archivierungsumgebung gestalten. Diese Umgebungen werden einen Spin-off auf die Forschungsinformation haben, weil dabei dieselbe Technologie angewendet wird. Im Zusammenhang mit dem Wechsel zu einem neuen Modell von hohem Volumen mit niedrigen Gewinnspannen statt des heutigen Modells von niedrigen Volumen mit hohen Gewinnspannen im Publikationsbereich entwickelt sich eine mehr symmetrische Rollenverteilung zwischen Universitaten und Verlagen in der Wertschopfungskette, die eine Fulle von Moglichkeiten der Vorwarts- und Ruckwartsintegration fur die Verlage ermoglicht.

Living cells are constantly subjected to a plethora of environmental stimuli that require integration into an appropriate cellular response. This integration takes place through signal transduction events that form tightly interconnected networks. The understanding of these networks requires to capture their dynamics through computational support and models. ANIMO (Analysis of Networks with Interactive MOdelling) is a tool that enables construction and exploration of executable models of biological networks, helping to derive hypotheses and to plan wet-lab experiments. The tool is based on the formalism of Timed Automata, which can be analysed via the UPPAAL model checker. Thanks to Timed Automata, we can provide a formal semantics for the domain-specific language used to represent signalling networks. This enforces precision and uniformity in the definition of signalling pathways, contributing to the integration of isolated signalling events into complex network models. We propose an approach to discretization of reaction kinetics that allows us to efficiently use UPPAAL as the computational engine to explore the dynamic behaviour of the network of interest. A user-friendly interface hides the use of Timed Automata from the user, while keeping the expressive power intact. Abstraction to single-parameter kinetics speeds up construction of models that remain faithful enough to provide meaningful insight. The resulting dynamic behaviour of the network components is displayed graphically, allowing for an intuitive and interactive modelling experience.

One of the vexing problems that besets concurrent use of multiple, heterogeneous resources is format multiplicity.C2M aims to equip scientists with a wrapper generator on their desktop. The wrapper generator can build wrappers, or converters that can convert data from or into different formats, from a high-level description of the formats. The language in which such a high-level description is expressed is easy enough for scientists to be able to write format descriptions at minimal cost. InC2M, wrappers and documentation for human reading are automatically obtained from the same user-supplied specifications. Initial experiments demonstrate that the idea can, indeed, lead to the advent of usergoverned wrapper generators. Future research will consolidate the code and extend the approach to a realistic variety of formats.

This article analyses the transformation of the value chain of scientific information in response to concomitant changes in scientific research and education. The scientific communication market is described in terms of main driving forces and their interplay. These forces are the actor (author/reader), accessibility, content, and applicability pairs. Scientific communication is described in this article in terms of its four functions: registration, archive, awareness, and certification. The introduction of these forces and functions allows a structural analysis of the scientific communication market and allows us to discuss aspects of structural continuity in, e.g., describing the transformation from a paper-based system to communication in a digital environment. The developments are seen to emphasise the already existing autonomous development towards a “unified archive”, lead us to review certification policies to include elements external to research and lead us to consider new structures for scientific communication, and publications. The new structures can be seen to result from the interactions in the market as modelled by the forces and the functions. The distinction between formal and informal communication is seen to become less useful. The need to review the structure and organisation of the market becomes evident, in particular if we consider communication during research and education as well. This leads us to speculate whether elements of the virtual organisation are of relevance.

Resolving conflicts between different measurements ofa property of a physical system may be a key step in a discoveryprocess. With the emergence of large-scale databases and knowledgebases with property measurements, computer support for the task ofconflict resolution has become highly desirable. We will describe amethod for model-based conflict resolution and the accompanyingcomputer tool KIMA, which have been applied in a case-study inmaterials science. In order to be a useful aid to scientists, the toolneeds to be integrated with other tools in a computer-supporteddiscovery environment. We will give an outline of such acomputer-supported discovery environment and argue that its use mightlead to new ways of doing science, so-called computer regimes.

On-line information retrieval systems often offer their users some means to tune the query to match the level of granularity of the information request. Users can be offered a far greater range of possibilities, however, if documents are indexed with coordinated index concepts. Coordinated index concepts are compound index concepts that express a relation between concepts that function as simple subject descriptors, as in cures(headache, aspirin). We show the point by giving a functional specification of a query engine that can handle both simple and coordinated index concepts, Boolean combinations, and superconcept expansion. The Condorcet Query Engine, a prototype query engine that can be run over the World Wide Web (WWW), demonstrates the feasibility of these ideas. The combination of known and novel techniques ensures a smooth migration path from existing query engines to more advanced engines that handle coordinated index concepts.

Ontologies are finding increasing use in all kinds of computer applications, and applications in biology are no exception. The main objective of this workshop was to bring together scientists of various disciplines, such as biologists, computer scientists, philosophers and computer linguists, who are working on, or are interested in, the development of ontologies in biology and related fields. We wanted to share experiences, methods, ontologies and tools. The invitation to the speakers mentioned four main questions to focus the discussion

Very big displays are now commonplace but interactions with them are limited, even poorly understood. Recently, understanding touch-based interactions have received a great deal of attention due to the popularity and low costs of these displays. The direct extension of such interactions, touch less interactions, has not. In this paper we evaluated gesture-based interactions with very big interactive screens to learn which gestures are suited and why. In other words, did ‘Minority Report’ get it right? We aim to discover to which extend these gesture interfaces are technology-driven and influenced by prototyped, commercial and fictive interfaces. A qualitative evaluation of a gesture interface for wall sized displays is presented in which subjects experienced the interface while completing several simple puzzle tasks. We found that simple gestures based on the act of pressing buttons was the most intuitive.

FeelSound is a multi-user application for collaboratively composing music in an entertaining way. Up to four composers can jointly create acoustic music on a top-projection multi-touch sensitive table. The notes of an acoustic instrument are represented on a harmonic table and, by drawing shapes on an instrument's table, a sample is created. These samples are then composed into a single score. FeelSound has been demonstrated in three public settings and it was able to entice passers-by to be musically artistic and creative.

This chapter addresses awareness support to enhance teamwork in co-located collaborative environments. In particular, the authors focus on the concept of situational awareness which is essential for successful team collaboration. Mutual situational awareness leads to informal social interactions, development of shared working cultures which are essential aspects of maintaining working relationships. First, an overview of the studies on team coordination and situational awareness support is presented. Second, a collaborative working environment is described for scientific teams in a molecular biology omics experimentation domain. Then, the results of practical case studies are discussed, as well as situational awareness support for scientific teams in collaborative environments. Finally, the authors discuss practical challenges in design and evaluation of group support systems for collaborative working environments and our multi-level analysis approach. The chapter gives new insights into how shared displays support group awareness, and how to design and evaluate interactive systems and visualisations that afford awareness in order to stimulate existing and new forms of collaboration in advanced working environments.

User interfaces in modern bioinformatics tools are designed for experts. They are too complicated for novice users such as bench biologists. This report presents the full results of a formative user study as part of a domain and requirements analysis to enhance user interfaces and collaborative environments for multidisciplinary teamwork. Contextual field observations, questionnaires and interviews with bioinformatics researchers of different levels of expertise and various backgrounds were performed in order to gain insight into their needs and working practices. The analysed results are presented as a user profile description and user requirements for designing user interfaces that support the collaboration of multidisciplinary research teams in scientific collaborative environments. Although the number of participants limits the generalisability of the findings, the combination of recurrent observations with other user analysis techniques in real-life settings makes the contribution of this user study novel.

We report from the second ESF Programme on Functional Genomics workshop on Data Integration, which covered topics including the status of biological pathways databases in existing consortia; pathways as part of bioinformatics infrastructures; design, creation and formalization of biological pathways databases; generating and supporting pathway data and interoperability of databases with other external databases and standards. Key issues emerging from the discussions were the need for continued funding to cover maintenance and curation of databases, the importance of quality control of the data in these resources, and efforts to facilitate the exchange of data and to ensure the interoperability of databases.

Natural scientists increasingly rely on web-based information resources. The speed with which these data will be brought to the scientist's desktop in the near future, however, makes only too clear that automated support for efficient and effective use is in its infancy. In fact, most data are still processed by a combination of manual work and ad hoc programming. We propose to alleviate some of the problems by means of a research environment: a web site with highly graphical user interface that allows transparent access to resources and performs a certain degree of fusion of the information found.

Background R is the statistical language commonly used by many life scientists in (omics) data analysis. At the same time, these complex analyses benefit from a workflow approach, such as used by the open source workflow management system Taverna. However, Taverna had limited support for R, because it supported just a few data types and only a single output. Also, there was no support for graphical output and persistent sessions. Altogether this made using R in Taverna impractical. Findings We have developed an R plugin for Taverna: RShell, which provides R functionality within workflows designed in Taverna. In order to fully support the R language, our RShell plugin directly uses the R interpreter. The RShell plugin consists of a Taverna processor for R scripts and an RShell Session Manager that communicates with the R server. We made the RShell processor highly configurable allowing the user to define multiple inputs and outputs. Also, various data types are supported, such as strings, numeric data and images. To limit data transport between multiple RShell processors, the RShell plugin also supports persistent sessions. Here, we will describe the architecture of RShell and the new features that are introduced in version 1.2, i.e.: i) Support for R up to and including R version 2.9; ii) Support for persistent sessions to limit data transfer; iii) Support for vector graphics output through PDF; iv)Syntax highlighting of the R code; v) Improved usability through fewer port types. Our new RShell processor is backwards compatible with workflows that use older versions of the RShell processor. We demonstrate the value of the RShell processor by a use-case workflow that maps oligonucleotide probes designed with DNA sequence information from Vega onto the Ensembl genome assembly. Conclusion Our RShell plugin enables Taverna users to employ R scripts within their workflows in a highly configurable way.