Paul E. van der Vet

Analysing Scientific Workflows: Why Workflows Not Only Connect Web Services

Life science workflow systems are developed to help life scientists to conveniently connect various programs and web services. In practice however, much time is spent on data conversion, because web services provided by different organisations use different data formats. We have analysed all the Taverna workflows available at the my Experiment web site on December 11, 2008. Our analysis of the tasks in these workflows shows several noticeable aspects: their number ranges from 1 to 70 tasks per workflow; 18% of the workflows consist of a single task.Of the tasks used are 22% web services; local services, i.e. tasks executed by the workflow system itself, are very popular and cover 57% of tasks; tasks implemented by the workflow designer, scripting tasks, are is also used often (14%). Our analysis shows that over 30\% of tasks are related to data conversion.

Changes in the value chain of scientific information: economic consequences for academic institutions

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.

Designing Workflows on the Fly Using e-BioFlow

Life scientists use workflow systems for service orchestration to design their computer based experiments. These workflow systems require life scientists to design complete workflows before they can be run. Traditional workflow systems not support the explorative research approach life scientists prefer. In life science, it often happens that few steps are known in advance. Even if these steps are known, connecting these tasks still remains difficult. We have extended the e-BioFlow workflow system with an ad-hoc editor to support on-the-fly workflow design. This ad-hoc editor enables an ad-hoc design of the workflow with no predetermined plan of the final workflow. Users can execute partial workflows and extend these workflows using intermediate results. The ad-hoc editor enables its users to explore data and tasks representing tools and web services, in order to debug the workflow and to optimise parameter settings. Furthermore, it guides its users to find and connect compatible tasks. The result is a new workflow editor that simplifies workflow design and that better fits the explorative research style life scientists prefer.

Modeling Biological Pathway Dynamics With Timed Automata

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 capturing their dynamics through computational support and models. ANIMO (analysis of Networks with Interactive Modeling) is a tool that enables the 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 analyzed via the UPPAAL model checker. Thanks to Timed Automata, we can provide a formal semantics for the domain-specific language used to represent signaling networks. This enforces precision and uniformity in the definition of signaling pathways, contributing to the integration of isolated signaling 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 behavior 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 behavior of the network components is displayed graphically, allowing for an intuitive and interactive modeling experience.

Gestures for large display control

The hands are highly suited to interact with large public displays. It is, however, not apparent which gestures come naturally for easy and robust use of the interface. We first explored how uninstructed users gesture when asked to perform basic tasks. Our subjects gestured with great similarity and readily produced gestures they had seen before; not necessarily in a human-computer interface. In a second investigation these and other gestures were rated by a hundred subjects. A gesture set for explicit command-giving to large displays emerged from these ratings. It is notable that for a selection task, tapping the index finger in mid-air, like with a traditional mouse, scored highest by far. It seems that the mouse has become a metaphor in everyday life.

Modelling biological pathway dynamics with Timed Automata

When analysing complex interaction networks occurring in biological cells, a biologist needs computational support in order to understand the effects of signalling molecules (e.g. growth factors, drugs). ANIMO (Analysis of Networks with Interactive MOdelling) is a tool that allows the user to create and explore 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 signalling event models into complex, crosstalk-driven networks. We propose an approach to discretization of reaction kinetics that allows us to efficiently use UPPAAL as the computational engine to explore the dynamic cell behaviour. A user friendly interface makes the use of Timed Automata completely transparent to the biologist, while keeping the expressive power intact. This allows to define relatively simple, yet faithful models of complex biological interactions. The resulting timed behaviour is displayed graphically, allowing for an intuitive and interactive modelling experience.

TeddIR: tangible information retrieval for children

Despite several efforts to make search engines more child-friendly, children still have trouble using systems that require keyboard input. We present TeddIR: a system using a tangible interface that allows children to search for books by placing tangible figurines and books they like/dislike in a green/red box, causing relevant results to be shown on a display. This way, issues with spelling and query formulation are avoided. A fully functional prototype was built and evaluated with children aged 6--8 at a primary school. The children understood TeddIR to a large extent and enjoyed the playful interaction.

Developments in scientific communication: Considerations on the value chain

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.

User-Evaluated Gestures for Touchless Interactions from a Distance

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.

Using R in Taverna: RShell v1.2

BackgroundR 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.FindingsWe 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.ConclusionOur RShell plugin enables Taverna users to employ R scripts within their workflows in a highly configurable way.