Phylesystem: a git-based data store for community-curated phylogenetic estimates

Motivation: Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al., 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy and reusability of the phylogenetic statements. Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves the ability of other researchers to reuse phylogenetic estimates. As the process of curating a published phylogenetic estimate is not error-free, retaining a full record of the provenance of edits to a tree is crucial for openness, allowing editors to receive credit for their work and making errors introduced during curation easier to correct. Results: Here, we report the development of software infrastructure to support the open curation of phylogenetic data by the community of biologists. The backend of the system provides an interface for the standard database operations of creating, reading, updating and deleting records by making commits to a git repository. The record of the history of edits to a tree is preserved by git’s version control features. Hosting this data store on GitHub (http://github.com/) provides open access to the data store using tools familiar to many developers. We have deployed a server running the ‘phylesystem-api’, which wraps the interactions with git and GitHub. The Open Tree of Life project has also developed and deployed a JavaScript application that uses the phylesystem-api and other web services to enable input and curation of published phylogenetic statements

The Fossil Calibration Database—A New Resource for Divergence Dating

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important—often least appreciated—step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for nonspecialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open-access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as a key pipeline for peer-reviewed calibrations to enter the databas

The Fossil Calibration Database, A New Resource for Divergence Dating

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important, and often least appreciated, step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for non- specialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open- access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as one key pipeline for peer-reviewed calibrations to enter the database

Towards an ethical ecology of international service learning

International Service-Learning (ISL) is a pedagogical activity that seeks to blend student learning with community engagement overseas and the development of a more just society. ISL programmes have grown as educational institutions and non-governmental organisations have sought to achieve the goal of developing ‘global citizens’. However, Service Learning (SL) in general and International Service-Learning (ISL) in particular remain deeply under theorised. These educational initiatives provide policy makers with a practical response to their quest for a ‘Big Society’and present alluring pedagogical approaches for Universities as they react to reforms in Higher Education and seek to enhance both the student learning experience and graduate employability. After outlining the development of ISL in policy and practice, this paper draws on the rich tradition of ISL at one British university to argue that ISL is a form of engagement that has the potential to be ethical in character although we identify a number of factors that militate against this. Our contention is that ISL which promotes rationaland instrumental learning represents a deficit model and we therefore conceptualise ISL here as a transformative learning experience that evinces distinctly aesthetic and even spiritual dimensions. Upon this theoretical groundwork we lay the foundations for conceptualizing ISL in ways that ensure its ethical integrity

Imagining an Imperial Modernity: Universities and the West African Roots of Colonial Development

© 2016 Informa UK Limited, trading as Taylor & Francis GroupThis article takes the formation and work of the ‘Elliot’ Commission on Higher Education in West Africa (1943–45) to reconsider the roots of British colonial development. Late colonial universities were major development projects, although they have rarely been considered as such. Focusing particularly on the Nigerian experience and the controversy over Yaba Higher College (founded 1934), the article contends that late colonial plans for universities were not produced in Britain and then exported to West African colonies. Rather, they were formed through interactions between agendas and ideas with roots in West Africa, Britain and elsewhere. These debates exhibited asymmetries of power but produced some consensus about university development. African and British actors conceptualised modern education by combining their local concerns with a variety of supra-local geographical frames for development, which included the British Empire and the individual colony. The British Empire did not in this case forestall development, but shaped the ways in which development was conceived

Methodologies for city-scale assessment of renewable energy generation potential to inform strategic energy infrastructure investment

In support of national and international policies to address climate change, local government actors across Europe and Asia are committed to reducing greenhouse gas emissions. Many recognise the contribution that decentralised renewable electricity production can bring towards reducing emissions whilst also generating revenue. However, these actors are often subject to significant financial pressures, meaning a reliable and compelling business case is needed to justify upfront investment. This article develops a method for rapid comparison of initial project viability for multiple city sites and installation options using data from wind and solar resource prediction techniques. In doing so, detailed resource assessments grounded in academic research are made accessible and useful for city practitioners. Long term average wind speeds are predicted using a logarithmic vertical wind profile. This employs detailed three-dimensional building data to estimate aerodynamic parameters for the complex urban surface. Solar resource is modelled using a Geographical Information System-based methodology. This establishes the location and geometry of roof structures to estimate insolation, whilst accounting for shading effects from other buildings and terrain features. Project viability for potential installations is assessed in terms of the net present value over the lifespan of the technology and associated Feed-in Tariff incentive. Discounted return on investment is also calculated for all sites. The methodology is demonstrated for a case study of 6,794 sites owned by Leeds City Council, UK. Results suggest significant potential for small-scale wind and solar power generation across council assets. A number of sites present a persuasive business case for investment, and in all cases, using the generated electricity on site improves financial viability. This indicates that initial installations should be sited at assets with high electricity demands. Overall, the work establishes a 2 methodology that enables large city-level asset holders to make strategic investment decisions across their entire portfolio, which are based on financial assessment of wind and solar generation potential accurate to the individual asset scale. Such tools could facilitate strategic planning within cities and help to ensure that investment in renewable energy is focused at the most viable sites. In addition, the methodology can assist with asset management at the city scale by identifying sites with a higher market value as a result of their potential for renewable energy generation than otherwise might be estimated

Perceptions of Depth Elicited by Occluded and Shearing Motions of Random Dots

A computer-controlled display of random dots was used to study perceptions of depth. In this display, a field of stationary random dots surrounded a rectangular area in which random dots moved with uniform velocity in a single direction. The boundaries of this rectangle did not move. When dot motion was perpendicular to the longer boundary of the rectangle (occluded motion), the rectangle seemed to be behind the stationary background surround. Motion parallel to the longer boundary of the rectangle (shearing motion) made it appear in front of the surround. The relative lengths of the sides of the rectangle determined which effect predominated. Thus, for motion perpendicular to the long axis of the rectangle the occlusion predominated and naive subjects reported that the central area seemed farther away than the surround. For shearing motion parallel to the long axis, the subjects reported that the rectangle was closer than the surround and the strength of both effects also depended on the length-to-width ratio of the rectangle. If there was occluded motion along the long axis, as the length-to-width ratio increased so did the likelihood that subjects would report seeing the rectangle behind the surround. Conversely, with shearing motion along the long axis, increasing the length-to-width ratio increased the likelihood that the rectangle would appear unambiguously in front of the surround. Some subjects integrated the two cues with the resulting perception being a rotating cylinder. The occlusion effect was stronger than the shearing effect. In fact, this ‘far’ depth effect was so powerful that it tended to override conflicting depth cues such as height in the visual field or stereopsis. The ‘near’ depth effect produced by shearing motion was definite but these other depth cues could often override it

Perceptions of Depth Elicited by Occluded and Shearing Motions of Random Dots

A computer-controlled display of random dots was used to study perceptions of depth. In this display, a field of stationary random dots surrounded a rectangular area in which random dots moved with uniform velocity in a single direction. The boundaries of this rectangle did not move. When dot motion was perpendicular to the longer boundary of the rectangle (occluded motion), the rectangle seemed to be behind the stationary background surround. Motion parallel to the longer boundary of the rectangle (shearing motion) made it appear in front of the surround. The relative lengths of the sides of the rectangle determined which effect predominated. Thus, for motion perpendicular to the long axis of the rectangle the occlusion predominated and naive subjects reported that the central area seemed farther away than the surround. For shearing motion parallel to the long axis, the subjects reported that the rectangle was closer than the surround and the strength of both effects also depended on the length-to-width ratio of the rectangle. If there was occluded motion along the long axis, as the length-to-width ratio increased so did the likelihood that subjects would report seeing the rectangle behind the surround. Conversely, with shearing motion along the long axis, increasing the length-to-width ratio increased the likelihood that the rectangle would appear unambiguously in front of the surround. Some subjects integrated the two cues with the resulting perception being a rotating cylinder. The occlusion effect was stronger than the shearing effect. In fact, this ‘far’ depth effect was so powerful that it tended to override conflicting depth cues such as height in the visual field or stereopsis. The ‘near’ depth effect produced by shearing motion was definite but these other depth cues could often override it

Direction-specific adaptation in area MT of the owl monkey

Single neurons were recorded in owl monkey middle temporal visual cortex (MT). Directional neurons showed direction-selective adaptation to pattern motion: responses to motion in the preferred direction were reduced by adaptation to motion in the preferred direction and enhanced by adaptation in the opposite direction. Non-directional neurons did not show significant adaptation