Robert Haines

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud

The Taverna workflow tool suite (http://www.taverna.org.uk) is designed to combine distributed Web Services and/or local tools into complex analysis pipelines. These pipelines can be executed on local desktop machines or through larger infrastructure (such as supercomputers, Grids or cloud environments), using the Taverna Server. In bioinformatics, Taverna workflows are typically used in the areas of high-throughput omics analyses (for example, proteomics or transcriptomics), or for evidence gathering methods involving text mining or data mining. Through Taverna, scientists have access to several thousand different tools and resources that are freely available from a large range of life science institutions. Once constructed, the workflows are reusable, executable bioinformatics protocols that can be shared, reused and repurposed. A repository of public workflows is available at http://www.myexperiment.org. This article provides an update to the Taverna tool suite, highlighting new features and developments in the workbench and the Taverna Server.

A practical toolkit for computational steering

Computational steering refers to the real-time interaction of a scientist with their running simulation code. Despite the many benefits associated with computational steering, its uptake to date has been limited. In this paper we discuss the reasons for this and how the computational steering library and associated tools developed as part of the RealityGrid project aim to tackle them. We describe the functionality of the steering library and the use of Grid services in constructing a generic, dynamic architecture for discovering, steering and connecting visualization software to running simulations. The use of on-line visualization for providing feedback to the scientist is described, including the ways in which it may be enhanced through tools such as Chromium and Access Grid. Finally, we illustrate the flexibility of our approach by describing the functionality that has been added to various simulation codes as part of the RealityGrid project.

A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control

Abstract The compilation and cleaning of data needed for analyses and prediction of species distributions is a time consuming process requiring a solid understanding of data formats and service APIs provided by biodiversity informatics infrastructures. We designed and implemented a Taverna-based Data Refinement Workflow which integrates taxonomic data retrieval, data cleaning, and data selection into a consistent, standards-based, and effective system hiding the complexity of underlying service infrastructures. The workflow can be freely used both locally and through a web-portal which does not require additional software installations by users.

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

BackgroundMaking forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as “Web services”) and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust “in silico” science. However, use of this approach in biodiversity science and ecology has thus far been quite limited.ResultsBioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible ‘virtual laboratory’, free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity.ConclusionsOur work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.

A Distributed Computing Architecture to Support Field Engineering in Networked Systems

Field workforces have to implement day-to-day control decisions to keep the large scale real-world systems (e. g. Water Distribution Systems) operational. However, existing customized Decision Support Tools (DSTs) for field workforces operate on static and predefined datasets, available in the workers’ devices. This results in planning control actions that may appear safe in the local context but can cause conflicts and disturbances elsewhere in the system. To enable informed decision making, we discuss a generic architecture that supports the development of dynamic predictive DSTs for the field workforces. The predictive DSTs would not only provide up-to-date information but also allow field workforces to perform ‘What-If’ simulations. We extend our previous work, on accessing simulations via lightweight mobile devices, by updating the ‘What-If’ simulations with the real-time Wireless Sensor Network (WSN) data and the scheduled future control actions. The calibration with the sensor network data enables the simulations to predict the real-time state of the system, while the incorporation of future control actions reduces the risk of unexpected feedback between different parts of the system. Hence, considering both the current and possible future state in simulations enables the field workforces to take informed control decisions in the real-world system.

The service architecture of the TeraGyroid experiment

We describe the service architecture of the successful TeraGyroid experiment. In particular we discuss the use of the open Grid service infrastructure (OGSI) to build the services used during the experiment and illustrate the problems we encountered.

Bringing simulation to engineers in the field: a Web 2.0 approach

Field engineers working on water distribution systems have to implement day-to-day operational decisions. Since pipe networks are highly interconnected, the effects of such decisions are correlated with hydraulic and water quality conditions elsewhere in the network. This makes the provision of predictive decision support tools (DSTs) for field engineers critical to optimizing the engineering work on the network. We describe how we created DSTs to run on lightweight mobile devices by using the Web 2.0 technique known as Software as a Service. We designed our system following the architectural style of representational state transfer. The system not only displays static geographical information system data for pipe networks, but also dynamic information and prediction of network state, by invoking and displaying the results of simulations running on more powerful remote resources.

Marine long-term biodiversity assessment suggests loss of rare species in the Skagerrak and Kattegat region

Studies of cumulative and long-term effects of human activities in the ocean are essential for developing realistic conservation targets. Here, we report the results of a recent national marine biodiversity inventory along the Swedish West coast between 2004 and 2009. The expedition revisited many historical localities that have been sampled with the same methods in the early twentieth century. We generated comparable datasets from our own investigation and the historical data to compare species richness, abundance, and geographic distribution of diversity. Our analysis indicates that the benthic ecosystems in the region have lost a large part of its original species richness over the last seven decades. We find evidence that especially rare species have disappeared. This process has caused a more homogenized community structure in the region and diminished historical biodiversity hotspots. We argue that the contemporary lack of rare species in the benthic ecosystems of the Kattegat and Skagerrak offers less opportunity to respond to environmental perturbations in the future and suggest improving the poor representation of rare species in the region. The study shows the value of biodiversity inventories as well as natural history collections in investigations of accumulated effects of anthropogenic activities and for re-establishing species-rich, productive, and resilient ecosystems.

ABC: Using Object Tracking to Automate Behavioural Coding

Video data of people interacting with devices contains rich information about human behaviour that can be used to design or improve user experience. As a first step, it must be interpreted -- or coded -- into a form that can be analyzed systematically. The coding process is currently performed manually, and it can be slow and difficult, and biased by subjectivity. This is particularly problematic when trying to obtain data that should be objective, such as the movements of a user in relation to a device. We describe Automated Behavioural Coding (ABC), an open source object tracking technique designed to log user and device movements, and then output positional data that can be used to model interaction. We validate the technique in a study of dual screen TV viewing, and show that the ABC tool is able to correctly classify the direction of gaze to the TV or tablet up to 95% of the time, in a fraction of the time it takes to capture this data manually.

Virtual science on the move: Interactive access to simulations on supercomputers

The concept that scientists and engineers should be able to monitor and control simulations running on supercomputers has been discussed and implemented since the late 1980s. The recent explosion in the variety and capabilities of mobile devices allows this access to be taken to a new level, since the simulations running on supercomputers can be accessed as users are moving around in their normal work activities. This means that they have to be able to connect and disconnect at will from the simulation running on the supercomputer, without disturbing its execution. We present a general framework for such “mobile supercomputing” within the framework of Web services standards. To illustrate the potential of our method, we present a particular application of this framework to provide a rich mobile interface to a lattice-Boltzmann simulation of complex fluids running on an IBM Blue Gene/Q supercomputer.