Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

BACKGROUND: Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. RESULTS: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (http://www.phylotastic.org), and a server image. CONCLUSIONS: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.

Computational Journalism: from Answering Question to Questioning Answers and Raising Good Questions

Our media is saturated with claims of ``facts'' made from data. Database research has in the past focused on how to answer queries, but has not devoted much attention to discerning more subtle qualities of the resulting claims, e.g., is a claim ``cherry-picking''? This paper proposes a Query Response Surface (QRS) based framework that models claims based on structured data as parameterized queries. A key insight is that we can learn a lot about a claim by perturbing its parameters and seeing how its conclusion changes. This framework lets us formulate and tackle practical fact-checking tasks --- reverse-engineering vague claims, and countering questionable claims --- as computational problems. Within the QRS based framework, we take one step further, and propose a problem along with efficient algorithms for finding high-quality claims of a given form from data, i.e. raising good questions, in the first place. This is achieved to using a limited number of high-valued claims to represent high-valued regions of the QRS. Besides the general purpose high-quality claim finding problem, lead-finding can be tailored towards specific claim quality measures, also defined within the QRS framework. An example of uniqueness-based lead-finding is presented for ``one-of-the-few'' claims, landing in interpretable high-quality claims, and an adjustable mechanism for ranking objects, e.g. NBA players, based on what claims can be made for them. Finally, we study the use of visualization as a powerful way of conveying results of a large number of claims. An efficient two stage sampling algorithm is proposed for generating input of 2d scatter plot with heatmap, evalutaing a limited amount of data, while preserving the two essential visual features, namely outliers and clusters. For all the problems, we present real-world examples and experiments that demonstrate the power of our model, efficiency of our algorithms, and usefulness of their results.

VizMaps: A Bayesian Topic Modeling Based PubMed Search Interface

A common challenge that users of academic databases face is making sense of their query outputs for knowledge discovery. This is exacerbated by the size and growth of modern databases. PubMed, a central index of biomedical literature, contains over 25 million citations, and can output search results containing hundreds of thousands of citations. Under these conditions, efficient knowledge discovery requires a different data structure than a chronological list of articles. It requires a method of conveying what the important ideas are, where they are located, and how they are connected; a method of allowing users to see the underlying topical structure of their search. This paper presents VizMaps, a PubMed search interface that addresses some of these problems. Given search terms, our main backend pipeline extracts relevant words from the title and abstract, and clusters them into discovered topics using Bayesian topic models, in particular the Latent Dirichlet Allocation (LDA). It then outputs a visual, navigable map of the query results.

Across the bridge: CLEF 2001 - Non-English monolingual retrieval. The French task.

This paper presents work on document retrieval based on first time participation in the CLEF 2001 monolingual retrieval task using French. The experiment findings indicated that Okapi, the text retrieval system in use, can successfully be used for non-English text retrieval. A lot of internal pre-processing is required in the basic search system for conversion into Okapi access formats. Various shell scripts were written to achieve the conversion in a UNIX environment, failure of which would significantly have impeded the overall performance. Based on the experiment findings using Okapi - originally designed for English - it was clear that, although most European languages share conventional word boundaries and variant word morphemes formed by the additon of suffixes, there is significant difference between French and English retrieval depending on the adaptation of indexing and search strategies in use. No sophisticated method for higher recall and precision such as stemming techniques, phrase translation or de-compounding was employed for the experiment and our results were suggestively poor. Future participation would include more refined query translation tools.

Representing the influence of signage on evacuation behavior within an evacuation model

Occupant interaction with signage systems is being introduced into evacuation simulations through the newly developed concept of the Visibility Catchment Area or VCA. In this article, we describe the concept of VCA and how it has been extended to incorporate the presence of physical obstructions and termination distance. The VCA concept is then linked to a prototype behavior model intended to represent the occupant's interaction with the signage system. The functionality and performance of the newly developed model is then demonstrated through the simulation of various evacuation scenarios within a hypothetical supermarket layout

Enhancing the usability of numerical models with case-based reasoning

Numerical models are important tools used in engineering fields to predict the behaviour and the impact of physical elements. There may be advantages to be gained by combining Case-Based Reasoning (CBR) techniques with numerical models. This paper considers how CBR can be used as a flexible query engine to improve the usability of numerical models. Particularly they can help to solve inverse and mixed problems, and to solve constraint problems. We discuss this idea with reference to the illustrative example of a pneumatic conveyor problem. The paper describes example problems faced by design engineers in this context and the issues that need to be considered in this approach. Solution of these problems require methods to handle constraints in both the retrieval phase and the adaptation phase of a typical CBR cycle. We show approaches to the solution of these problesm via a CBR tool.

Experimental study and theoretical analysis of signage legibility distances as a function of observation angle

Signage systems are widely used in buildings to provide information for wayfinding, thereby assisting in navigation during normal circulation of pedestrians and, more importantly, exiting information during emergencies. An important consideration in determining the effectiveness of signs is establishing the region from which the sign is visible to occupants, the so-called Visibility Catchment Area (VCA). This paper attempts to factor into the determination of the VCA of signs, the observation angle of the observer using both experimental and theoretical analysis.

Signage legibility distances as a function of observation angle

Signage systems are widely used in buildings to provide information for wayfinding, thereby assisting in navigation during normal circulation of pedestrians and, more importantly, exiting information during emergencies. An important consideration in determining the effectiveness of signs is establishing the region from which the sign is visible to occupants, the so-called visibility catchment area (VCA). This study attempts to factor into the determination of the VCA of signs, the observation angle of the observer. In building regulations, it is implicitly assumed that the VCA is independent of the observation angle. A theoretical model is developed to explain the relationship between the VCA and observation angle and experimental trials are performed in order to assess the validity of this model. The experimental findings demonstrate a consistency with the theoretical model. Given this result, the functionality of a comprehensive evacuation model is extended in accordance with the assumptions on which the theoretical model is based and is then demonstrated using several examples

Simulating the interaction of occupants with signage systems

This paper describes the introduction of chained signage systems into evacuation simulation models. Signage systems are widely used in buildings to provide information for wayfinding, thereby providing exiting information during emergencies and assisting in navigation during normal circulation of pedestrians. Recently a system was developed to introduce simple signs into egress models. The system, known as Visibility Catchment Area or VCA, allowed similated agents to interact with signs which point directly to an exit and signs which are located directly above the exit. However, this approach was not able to represent the more general situation of a sign netwokr within an arbitrarily complex building. In this paper we extend the method to include chained signage systems which provides simulated agents that are unfamiliar with the structure a means by which to navigate to an emergency exit. The model includes the associated navigation behaviours exhibited by occupants that rely on a signage system for navigation including: Searching behaviours, Backtracking behaviours, Lost behaviours and Communication behaviours. The new features are demonstrated through a series of demonstration cases and are shown to produce plausible results.

Spaces of observation and obscurity: cinematic prisons of light and dark

In The Eye of Power, Foucault delineated the key concerns surrounding hospital architecture in the latter half of the eighteenth century as being the ‘visibility of bodies, individuals and things'. As such, the ‘new form of hospital' that came to be developed ‘was at once the effect and support of a new type of gaze'. This was a gaze that was not simply concerned with ways of minimising overcrowding or cross-contamination. Rather, this was a surveillance intended to produce knowledge about the pathological bodies contained within the hospital walls. This would then allow for their appropriate classification. Foucault went on to describe how these principles came to be applied to the architecture of prisons. This was exemplified for him in the distinct shape of Bentham's panopticon. This circular design, which has subsequently become an often misused synonym for a contemporary culture of surveillance, was premised on a binary of the seen and the not-seen. An individual observer could stand at the central point of the circle and observe the cells (and their occupants) on the perimeter whilst themselves remaining unseen. The panopticon in its purest form was never constructed, yet it conveys the significance of the production of knowledge through observation that became central to institutional design at this time and modern thought more broadly. What is curious though is that whilst the aim of those late eighteenth century buildings was to produce wellventilated spaces suffused with light, this provoked an interest in its opposite. The gothic movement in literature that was developing in parallel conversely took a ‘fantasy world of stone walls, darkness, hideouts and dungeons…' as its landscape (Vidler, 1992: 162). Curiously, despite these modern developments in prison design, the façade took on these characteristics. The gothic imagination came to describe that unseen world that lay behind the outer wall. This is what Evans refers to as an architectural ‘hoax'. The façade was taken to represent the world within the prison walls and it was the façade that came to inform the popular imagination about what occurred behind it. The rational, modern principles ordering the prison became conflated with the meanings projected by and onto the façade. This confusion of meanings have then been repeated and reenforced in the subsequent representations of the prison. This is of paramount importance since it is the cinematic and televisual representation of the prison, as I argue here and elsewhere, that maintain this erroneous set of meanings, this ‘hoax'.

Acceptance angle effects on the beam attenuation in the ocean

The beam attenuation serves as a proxy for particulate matter and is a key parameter in visibility algorithms for the aquatic environment. It is well known, however, that the beam attenuation is a function of the acceptance angle of the transmissometer used to measure it. Here we compare eight different transmissometers with four different acceptance angles using four different deployment strategies and sites, and find that their mean attenuation values differ markedly and in a consistent way with instrument acceptance angle: smaller acceptance angles provide higher beam attenuation values. This difference is due to variations in scattered light collected with different acceptance angles and is neither constant nor easy to parameterize. Variability (in space or time) in the ratios of beam attenuations measured by two different instruments correlates, in most cases, with the particle size parameter (as expected from Mie theory), but this correlation is often weak and can be the opposite of expectations based on particle size changes. We recommended careful consideration of acceptance angle in applications of beam transmission data especially when comparing data from different instruments. (C) 2009 Optical Society of America

Valuation of ecological and amenity impacts of an offshore windfarm as a factor in marine planning

Integrated marine planning, which must take into consideration environmental and social impacts, is being introduced widely in Europe, the USA, Australia and elsewhere. Installation of offshore windfarms creates impacts both on local marine ecosystems and the view of the seascape and is one of multiple activities in the marine area that must be addressed by marine planning. The impacts on people's values (and hence welfare) of changes in ecology and amenity that could arise from the installation of a windfarm in the Irish Sea were assessed using a discrete choice experiment administered through an online survey. The ecological changes investigated were: increased species diversity resulting from artificial reef effects, and the effect of electromagnetic fields from subsea cables on marine life; whilst the amenity change was the visibility of offshore turbines from land. Respondents expressed preferences for ecological improvements but had less clear preferences regarding the height and visibility of the turbines. In particular distance decay effects were observed with respondents further away from the coast being less concerned about visual impact created by offshore turbines. Understanding ecological and amenity impacts and how they are valued by people can support the decisions made within marine planning and licensing.

Las bibliotecas rurales en los medios de comunicación de la Región de Extremadura: un estudio de caso

El objetivo principal de este trabajo es, a través de las noticias publicadas en diversos medios de comunicación de la Región de Extremadura sobre bibliotecas rurales a lo largo de los últimos años, comprobar el impacto y la visibilidad de las bibliotecas en los medios. Para ello, se recopilan un total de 1196 noticias que, tras ser analizadas detalladamente, se reducen a 300 sobre las que versan los resultados del estudio. Esta disminución de noticias finales demuestra que el titular o los primeros párrafos no expresan exactamente el contenido de la noticia siendo necesario un análisis cualitativo de su contenido. Se concluye que: las noticias sobre bibliotecas rurales han decrecido en el periodo analizado (2007, 2008, 2012, 2013), siendo 2007 el año de mayor auge, si bien se ha observado un repunte en 2013 con respecto a 2012; las noticias sobre bibliotecas rurales de ámbito provincial (Badajoz y Cáceres) obtienen mayor porcentaje que las regionales y nacionales (sin representación); y el diario HOY es, con diferencia, el medio que acumula el mayor porcentaje de noticias sobre bibliotecas rurales.

Making Risk Visible. The role of images in the assessment of (cancer) genetic risk

Whilst analysis of 'risk' (in its many conceptual shapes) has loomed large in both medicine and social sciences over the past 25 years, detailed investigations as to how risk assessments are actually put together (in either lay or professional contexts) are few in number. The studies that are available usually focus on the use of words or everyday conversation in assembling risk. Talking about risk is, of course, important, but what tends to be ignored is the fact that risk can be and is often made visible. For example, it can be made visible through the use of tables, charts, diagrams and various kinds of sophisticated laboratory images. This paper concentrates on the role of such images in the context of a cancer genetics clinic and its associated laboratory. Precisely how these images are tied into the production of risk estimates, how professionals discuss and use such images in clinical work, and how professionals reference them to display facts about risk is the focus of the paper. The paper concludes by highlighting the significance of different kinds of visibility for an understanding of genetic abnormalities and how such differences might impact on the attempts of lay people to get to grips with risk.

Development of Illusory contour perception in infants

We investigated whether infants from 8 ^ 22 weeks of age were sensitive to the illusory contour created by aligned line terminators. Previous reports of illusory-contour detection in infants under 4 months old could be due to infants' preference for the presence of terminators rather than their configuration. We generated preferential-looking stimuli containing sinusoidal lines whose oscillating, abutting terminators give a strong illusory contour in adult perception. Our experiments demonstrated a preference in infants 8 weeks old and above for an oscillating illusory contour compared with a stimulus containing equal terminator density and movement. Control experiments excluded local line density, or attention to alignment in general, as the basis for this result. In the youngest age group (8 ^ 10 weeks) stimulus velocity appears to be critical in determining the visibility of illusory contours, which is consistent with other data on motion processing at this age. We conclude that, by 2 months of age, the infant's visual system contains the nonlinear mechanisms necessary to extract an illusory contour from aligned terminators.