Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation

Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract part of this information but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIY ABC) for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIY ABC can be used to compare competing scenarios, estimate parameters for one or more scenarios and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real dataset, both with complex evolutionary scenarios, illustrates the main possibilities of DIY ABC.

User-friendly free-text keystroke dynamics authentication for practical applications

This paper introduces a novel approach for free-text keystroke dynamics authentication which incorporates the use of the keyboard’s key-layout. The method extracts timing features from specific key-pairs. The Euclidean distance is then utilized to find the level of similarity between a user’s profile data and his/her test data. The results obtained from this method are reasonable for free-text authentication while maintaining the maximum level of user relaxation. Moreover, it has been proven in this study that flight time yields better authentication results when compared with dwell time. In particular, the results were obtained with only one training sample for the purpose of practicality and ease of real life application.

An economic decision support tool for simulating paratuberculosis control strategies in a UK suckler beef herd

A dynamic, deterministic, economic simulation model was developed to estimate the costs and benefits of controlling Mycobacterium avium subsp. paratuberculosis (Johne's disease) in a suckler beef herd. The model is intended as a demonstration tool for veterinarians to use with farmers. The model design process involved user consultation and participation and the model is freely accessible on a dedicated website. The 'user-friendly' model interface allows the input of key assumptions and farm specific parameters enabling model simulations to be tailored to individual farm circumstances. The model simulates the effect of Johne's disease and various measures for its control in terms of herd prevalence and the shedding states of animals within the herd, the financial costs of the disease and of any control measures and the likely benefits of control of Johne's disease for the beef suckler herd over a 10-year period. The model thus helps to make more transparent the 'hidden costs' of Johne's in a herd and the likely benefits to be gained from controlling the disease. The control strategies considered within the model are 'no control', 'testing and culling of diagnosed animals', 'improving management measures' or a dual strategy of 'testing and culling in association with improving management measures'. An example 'run' of the model shows that the strategy 'improving management measures', which reduces infection routes during the early stages, results in a marked fall in herd prevalence and total costs. Testing and culling does little to reduce prevalence and does not reduce total costs over the 10-year period.

Exploiting CAFS-ISP

In the summer of 1982, the ICLCUA CAFS Special Interest Group defined three subject areas for working party activity. These were: 1) interfaces with compilers and databases, 2) end-user language facilities and display methods, and 3) text-handling and office automation. The CAFS SIG convened one working party to address the first subject with the following terms of reference: 1) review facilities and map requirements onto them, 2) "Database or CAFS" or "Database on CAFS", 3) training needs for users to bridge to new techniques, and 4) repair specifications to cover gaps in software. The working party interpreted the topic broadly as the data processing professional's, rather than the end-user's, view of and relationship with CAFS. This report is the result of the working party's activities. The report content for good reasons exceeds the terms of reference in their strictest sense. For example, we examine QUERYMASTER, which is deemed to be an end-user tool by ICL, from both the DP and end-user perspectives. First, this is the only interface to CAFS in the current SV201. Secondly, it is necessary for the DP department to understand the end-user's interface to CAFS. Thirdly, the other subjects have not yet been addressed by other active working parties.

Solving surface structures from normal incidence X-ray standing wave data

A program is provided to determine structural parameters of atoms in or adsorbed on surfaces by refinement of atomistic models towards experimentally determined data generated by the normal incidence X-ray standing wave (NIXSW) technique. The method employs a combination of Differential Evolution Genetic Algorithms and Steepest Descent Line Minimisations to provide a fast, reliable and user friendly tool for experimentalists to interpret complex multidimensional NIXSW data sets.

Object-based three-dimensional X-ray imaging

A form of three-dimensional X-ray imaging, called Object 3-D, is introduced, where the relevant subject material is represented as discrete ‘objects’. The surface of each such object is derived accurately from the projections of its outline, and of its other discontinuities, in about ten conventional X-ray views, distributed in solid angle. This technique is suitable for many applications, and permits dramatic savings in radiation exposure and in data acquisition and manipulation. It is well matched to user-friendly interactive displays.

Suitability of pesticide risk indicators for less developed countries: a comparison

Pesticide risk indicators provide simple support in the assessment of environmental and health risks from pesticide use, and can therefore inform policies to foster a sustainable interaction of agriculture with the environment. For their relative simplicity, indicators may be particularly useful under conditions of limited data availability and resources, such as in Less Developed Countries (LDCs). However, indicator complexity can vary significantly, in particular between those that rely on an exposure–toxicity ratio (ETR) and those that do not. In addition, pesticide risk indicators are usually developed for Western contexts, which might cause incorrect estimation in LDCs. This study investigated the appropriateness of seven pesticide risk indicators for use in LDCs, with reference to smallholding agriculture in Colombia. Seven farm-level indicators, among which 3 relied on an ETR (POCER, EPRIP, PIRI) and 4 on a non-ETR approach (EIQ, PestScreen, OHRI, Dosemeci et al., 2002), were calculated and then compared by means of the Spearman rank correlation test. Indicators were also compared with respect to key indicator characteristics, i.e. user friendliness and ability to represent the system under study. The comparison of the indicators in terms of the total environmental risk suggests that the indicators not relying on an ETR approach cannot be used as a reliable proxy for more complex, i.e. ETR, indicators. ETR indicators, when user-friendly, show a comparative advantage over non-ETR in best combining the need for a relatively simple tool to be used in contexts of limited data availability and resources, and for a reliable estimation of environmental risk. Non-ETR indicators remain useful and accessible tools to discriminate between different pesticides prior to application. Concerning the human health risk, simple algorithms seem more appropriate for assessing human health risk in LDCs. However, further research on health risk indicators and their validation under LDC conditions is needed.

Non-visual and multisensory BCI systems: present and future

During the past decade, brain–computer interfaces (BCIs) have rapidly developed, both in technological and application domains. However, most of these interfaces rely on the visual modality. Only some research groups have been studying non-visual BCIs, primarily based on auditory and, sometimes, on somatosensory signals. These non-visual BCI approaches are especially useful for severely disabled patients with poor vision. From a broader perspective, multisensory BCIs may offer more versatile and user-friendly paradigms for control and feedback. This chapter describes current systems that are used within auditory and somatosensory BCI research. Four categories of noninvasive BCI paradigms are employed: (1) P300 evoked potentials, (2) steady-state evoked potentials, (3) slow cortical potentials, and (4) mental tasks. Comparing visual and non-visual BCIs, we propose and discuss different possible multisensory combinations, as well as their pros and cons. We conclude by discussing potential future research directions of multisensory BCIs and related research questions

User interface standards for expert systems: are they appropriate?

In recent years there has been a growing debate over whether or not standards should be produced for user system interfaces. Those in favor of standardization argue that standards in this area will result in more usable systems, while those against argue that standardization is neither practical nor desirable. The present paper reviews both sides of this debate in relation to expert systems. It argues that in many areas guidelines are more appropriate than standards for user interface design.

A web 2.0 user interface for wide-area resource monitoring

Resource monitoring in distributed systems is required to understand the 'health' of the overall system and to help identify particular problems, such as dysfunctional hardware or faulty system or application software. Monitoring systems such as GridRM provide the ability to connect to any number of different types of monitoring agents and provide different views of the system, based on a client's particular preferences. Web 2.0 technologies, and in particular 'mashups', are emerging as a promising technique for rapidly constructing rich user interfaces, that combine and present data in intuitive ways. This paper describes a Web 2.0 user interface that was created to expose resource data harvested by the GridRM resource monitoring system.

PRISM and ENES: a European approach to Earth system modelling

Europe's widely distributed climate modelling expertise, now organized in the European Network for Earth System Modelling (ENES), is both a strength and a challenge. Recognizing this, the European Union's Program for Integrated Earth System Modelling (PRISM) infrastructure project aims at designing a flexible and friendly user environment to assemble, run and post-process Earth System models. PRISM was started in December 2001 with a duration of three years. This paper presents the major stages of PRISM, including: (1) the definition and promotion of scientific and technical standards to increase component modularity; (2) the development of an end-to-end software environment (graphical user interface, coupling and I/O system, diagnostics, visualization) to launch, monitor and analyse complex Earth system models built around state-of-art community component models (atmosphere, ocean, atmospheric chemistry, ocean bio-chemistry, sea-ice, land-surface); and (3) testing and quality standards to ensure high-performance computing performance on a variety of platforms. PRISM is emerging as a core strategic software infrastructure for building the European research area in Earth system sciences. Copyright (c) 2005 John Wiley & Sons, Ltd.

Toward construction of an inexpensive brain computer interface for goal oriented applications

The paper describes the implementation of an offline, low-cost Brain Computer Interface (BCI) alternative to more expensive commercial models. Using inexpensive general purpose clinical EEG acquisition hardware (Truscan32, Deymed Diagnostic) as the base unit, a synchronisation module was constructed to allow the EEG hardware to be operated precisely in time to allow for recording of automatically time stamped EEG signals. The synchronising module allows the EEG recordings to be aligned in stimulus time locked fashion for further processing by the classifier to establish the class of the stimulus, sample by sample. This allows for the acquisition of signals from the subject’s brain for the goal oriented BCI application based on the oddball paradigm. An appropriate graphical user interface (GUI) was constructed and implemented as the method to elicit the required responses (in this case Event Related Potentials or ERPs) from the subject.

User's manual

'Typeform dialogues', as originally planned for publication, was an interactive CD-based screen interface presenting a comparative survey of typeform history and description. The CD was to be held inside a printed book that included two essays and a User’s Manual. Although 'Typeform dialogues' (CD+book) was not completed as planned, a PDF file was published containing the User’s Manual, together with background information about the interface and the project it was part of. The User's Manual presents all interface sections and features (using screen grabs) and explains their editorial rationale, design, and function.