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There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For more than a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for these tools to make them accessible to a wide range of researchers. To streamline the process of integrating tools and constructing workflows as much as possible, we have developed Planemo, a software development kit for tool and workflow developers and Galaxy power users. Here we outline Planemo's implementation and describe its broad range of functionality for designing, testing, and executing Galaxy tools, workflows, and training material. In addition, we discuss the philosophy underlying Galaxy tool and workflow development, and how Planemo encourages the use of development best practices, such as test-driven development, by its users, including those who are not professional software developers.

In most countries, buildings are responsible for significant energy consumption where space heating and air conditioning is responsible for the majority of this energy use. To reduce this massive consumption and decrease carbon emission, thermal insulation of buildings can play an important role. The estimation of energy savings following the improvement of a building's insulation remains a key area of research in order to calculate the cost savings and the payback period. In this paper, a case study has been presented where deep retrofitting has been introduced to an existing building to bring it closer to a Passivhaus standard with the introduction of insulation and solar photovoltaic panels. The thermal performance of the building with its improved insulation has been evaluated using infrared thermography. Artificial intelligence using deep learning neural networks is implemented to predict the thermal performance of the building and the expected energy savings. The prediction of neural networks is compared with the actual savings calculated using historical weather data. The results of the neural network show high accuracy of predicting the actual energy savings with success rate of about 82% when compared with the calculated values. The results show that this suggested approach can be used to rapidly predict energy savings from retrofitting of buildings with reasonable accuracy, hence providing a practical rapid tool for the building industry and communities to estimate energy savings. A mathematical model has been also developed which has indicated a life-long monitoring will be needed to precisely estimate the benefits of energy savings in retrofitting due to the change in weather conditions and people's behaviour.

There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For over a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for these tools to make them accessible to a wide range of researchers. In order to streamline the process of integrating tools and constructing workflows as much as possible, we have developed Planemo, a software development kit for tool and workflow developers and Galaxy power users. Here we outline Planemo’s implementation and describe its broad range of functionality for designing, testing and executing Galaxy tools, workflows and training material. In addition, we discuss the philosophy underlying Galaxy tool and workflow development, and how Planemo encourages the use of development best practices, such as test-driven development, by its users, including those who are not professional software developers. Planemo is a mature project widely used within the Galaxy community which has been downloaded over 80,000 times.

SummaryThe existence of more than 100 public Galaxy servers with service quotas is indicative of the need for an increased availability of compute resources for Galaxy to use. The GalaxyCloudRunner enables a Galaxy server to easily expand its available compute capacity by sending user jobs to cloud resources. User jobs are routed to the acquired resources based on a set of configurable rules and the resources can be dynamically acquired from any of 4 popular cloud providers (AWS, Azure, GCP, or OpenStack) in an automated fashion.Availability and implementationGalaxyCloudRunner is implemented in Python and leverages Docker containers. The source code is MIT licensed and available at https://github.com/cloudve/galaxycloudrunner. The documentation is available at http://gcr.cloudve.org/.ContactEnis Afgan (enis.afgan@jhu.edu)Supplementary informationNone

Whilst the evidence for the efficacy of treatment interventions for individuals with dual diagnosis has been developing in recent decades, little is known about individual perceptions and the personal benefits of attending integrated treatment programmes within this population group. A qualitative methodology, Interpretive phenomenological analysis, was used to investigate the experiences of individuals with a range of complex mental health and coexisting substance misuse problems who took part in a psychoeducational group (PEG) programme. This comprised of social support and therapeutic peer group relationship facilitation. Semi-structured interviews were undertaken with 15 service users who successfully participated in this treatment programme. Findings identify the complexity of the therapeutic process and understanding of the treatment from the service users perspective. This included the importance of forming meaningful therapeutic relationships as an influential factor in countering a range of distressing and incompatible environmental and situational stressors, such as self-regulatory control, self-awareness of a need for change and the importance of integrated treatment in reducing the sense of stigma and exclusion linked with using mental health services. The study findings support the use of integrated treatment programmes in mental health services with a dual diagnosis population group.

Computational Workflows are widely used in data analysis, enabling innovation and decision-making. In many domains (bioinformatics, image analysis, & radio astronomy) the analysis components are numerous and written in multiple different computer languages by third parties. However, many competing workflow systems exist, severely limiting portability of such workflows, thereby hindering the transfer of workflows between different systems, between different projects and different settings, leading to vendor lock-ins and limiting their generic re-usability. Here we present the Common Workflow Language (CWL) project which produces free and open standards for describing command-line tool based workflows. The CWL standards provide a common but reduced set of abstractions that are both used in practice and implemented in many popular workflow systems. The CWL language is declarative, which allows expressing computational workflows constructed from diverse software tools, executed each through their command-line interface. Being explicit about the runtime environment and any use of software containers enables portability and reuse. Workflows written according to the CWL standards are a reusable description of that analysis that are runnable on a diverse set of computing environments. These descriptions contain enough information for advanced optimization without additional input from workflow authors. The CWL standards support polylingual workflows, enabling portability and reuse of such workflows, easing for example scholarly publication, fulfilling regulatory requirements, collaboration in/between academic research and industry, while reducing implementation costs. CWL has been taken up by a wide variety of domains, and industries and support has been implemented in many major workflow systems., 8 pages, 3 figures. For the LaTex source code of this paper, see https://github.com/mr-c/cwl_methods_included

This chapter first provides a concise account of the basic principles and concepts underlying scientific groundwater management, and it then both summarises the policy approach to developing an adaptive scheme of management and protection for groundwater resources that is appropriately integrated across relevant sectors and assesses the governance needs, roles and planning requirements to implement the selected policy approach.

Study region: pan-Europe, from Western Europe to Central Asia. Study focus: Knowledge of transboundary aquifers (TBAs) in the pan-European region has evolved through an inventory under the Convention on the Protection and Use of Transboundary Watercourses and International Lakes (Water Convention) completed in 1999, and the First and Second Assessments of transboundary waters undertaken in 2007 and 2011. These “snapshots”, together with intergovernmental review processes indicate significant advances in the recognition of TBAs. Reference is made to where collaboration on transboundary groundwaters has developed, demonstrated by cooperation arrangements and joint projects. New hydrological insights for the region: The findings highlight a number of factors; inventories, participation in the work of the Water Convention and application of guidelines, joint projects, the legal and institutional framework for management and the role of EU legislation. There is a need for sound conceptual hydrogeological models of TBAs, but also for broadening joint assessment to better foster cooperation. Bringing together in transboundary dialogues technical information with an understanding of the demands for groundwater and related drivers as well as better understanding of the human, social and institutional dimensions of managing TBAs can add to their effectiveness. Such approaches can better provide for defining and discussing policy responses and for mobilising resources and the necessary political support. Keywords: Water resources, Groundwater, Convention, Governance, Assessment, Monitoring, Transboundary cooperation

This paper reports on the daylighting performance of switchable ethylene-tetrafluoroethylene (ETFE) foil in double-skin façades (DSF). In contrast to conventional glazing or static ETFE façades, switchable ETFE moderates incident daylight and controls internal light distribution by actively responding to weather conditions and solar light intensity. To better understand the light control function of ETFE and the impact of parameters such as climate, latitude and window-to-wall ratios (WWR), a validated optical model was used to evaluate different DSF designs. ETFE façades were modelled with a Bidirectional-scattering distribution-function (BSDF) and spectral data, obtained from experimental measurements, to accurately represent specular and diffuse light transmittance. Based on the five-phase method, a parametric climate data-driven simulation of an office room with different façade designs was conducted for three climate scenarios (Oceanic, Mediterranean, Sub-Tropical). When employing switchable ETFE in façades with different WWRs (30–90%), an annual increase of useful daylight illuminance (UDI) from 11 to 69% in the range of 500–2000lx was recorded. The calculated glare probability (DGPs) declined 59% in the best-case scenarios, providing working conditions with imperceptible glare for 94% of the scheduled time. Simultaneously, the daylight uniformity ratio (UR) increased up to 19% compared to a room with a conventional double-glazed façade. Significant improvements of daylight quality were achieved for façades with large windows in climates with abundant solar light available all year long. Overall, this study contributes to expanding the knowledge on adaptive membrane façades, demonstrating their capacity to enhance the daylighting performance of indoor spaces in different climates.

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, management, and analysis. In this perspective, we present AnVIL, describe its ecosystem and interoperability with other platforms, and highlight how this platform and associated initiatives contribute to improved genomic data sharing efforts. The AnVIL is a federated cloud platform designed to manage and store genomics and related data, enable population-scale analysis, and facilitate collaboration through the sharing of data, code, and analysis results. By inverting the traditional model of data sharing, the AnVIL eliminates the need for data movement while also adding security measures for active threat detection and monitoring and provides scalable, shared computing resources for any researcher. We describe the core data management and analysis components of the AnVIL, which currently consists of Terra, Gen3, Galaxy, RStudio/Bioconductor, Dockstore, and Jupyter, and describe several flagship genomics datasets available within the AnVIL. We continue to extend and innovate the AnVIL ecosystem by implementing new capabilities, including mechanisms for interoperability and responsible data sharing, while streamlining access management. The AnVIL opens many new opportunities for analysis, collaboration, and data sharing that are needed to drive research and to make discoveries through the joint analysis of hundreds of thousands to millions of genomes along with associated clinical and molecular data types.

Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended. During the last two years, the Galaxy team and the open-source community around Galaxy have made substantial improvements to Galaxy's core framework, user interface, tools, and training materials. Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed. The Galaxy community has led an effort to create numerous high-quality tutorials focused on common types of genomic analyses. The Galaxy developer and user communities continue to grow and be integral to Galaxy's development. The number of Galaxy public servers, developers contributing to the Galaxy framework and its tools, and users of the main Galaxy server have all increased substantially.

This concise international review focuses on policy experience with the protection of groundwater against diffuse pollution—one of today’s greatest environmental challenges. Diffuse pollution encompasses those forms of contaminant load generation, such as agricultural land use practices and urban housing in situ sanitation, that occur on a widespread geographical basis. This cannot be tackled directly through legislation but must be addressed by implementing land use control policies with the relevant stakeholders in appropriate zones. The review also looks at the technical advances in defining priority land areas for protection together with the selection of practical measures for controlling agricultural practices and urban in situ sanitation.

The current state of much of the Wuhan pneumonia virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) research shows a regrettable lack of data sharing and considerable analytical obfuscation. This impedes global research cooperation, which is essential for tackling public health emergencies and requires unimpeded access to data, analysis tools, and computational infrastructure. Here, we show that community efforts in developing open analytical software tools over the past 10 years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an open and transparent manner. Specifically, we use all SARS-CoV-2 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and (2) demonstrate that existing community efforts in curation and deployment of biomedical software can reliably support rapid, reproducible research during global health crises. All our analyses are fully documented at https://github.com/galaxyproject/SARS-CoV-2.

This paper presents a detailed structural analysis of a bubble shell engineered by Heinz Isler. Through 3D scanning the geometry of this shell structure has become available to the authors. Structural analysis has not been possible before since the geometry of the shell was not available. The bubble shell was Isler’s most built type of shell. In the paper first the process of reverse engineering the geometry of the shell is described. Second, the effect of pre-stress in the edge beams is described. Third, the load distribution throughout the shell and the membrane behaviour relative to bending behaviour is assessed.

Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. But ensuring that the methods evaluated are reproducible and reusable is complicated by the diversity of software architectures, input and output file formats, and computing environments. To mitigate these problems, some challenges have leveraged new virtualization and compute methods, requiring participants to submit cloud-ready software packages. We review recent data challenges with innovative approaches to model reproducibility and data sharing, and outline key lessons for improving quantitative biomedical data analysis through crowd-sourced benchmarking challenges. Electronic supplementary material The online version of this article (10.1186/s13059-019-1794-0) contains supplementary material, which is available to authorized users.

Interoperability of datasets, tools, and resources is essential to modern scientific investigation and analysis. The necessity to gather disparate datasets together, perform analysis with a collection of discrete tools, and visualize the results remains a standard approach for exploring and making sense across scientific research domains. Here, we describe the Galaxy External Display Application (GEDA) framework which provides researchers with the ability to facilitate the interoperability of Galaxy user data and external resources, while promoting findability, accessibility, and reuse. The only requirement on the external resource for GEDA accessibility is that it is able to accept a parameter value that contains a URL pointing to user data.

Conventionally, technology-based articles focus on methods by which architects and\ud engineers designed and built to present new methods, materials to evidence novelty in\ud technical terms. This paper does not do that. Instead, through a current overview of past and\ud present timber practices, it will present a new cultural perspective by looking at timber\ud technology from purist and liberalist approaches. Indicating a moralistic sensibility of what\ud "constructing correctly" in wood means to them, with these two attitudes implying inherent\ud values, this paper seeks to project a new cultural dimension on technology. More\ud importantly, the approaches convincingly reflects our relationship with digital technology, as\ud timber culture and tradition come to terms with the inevitability of the digital age.

A pneumatic multilayer foil construction with a kinetic shading mechanism has the potential to be an effective response to dynamic climatic factors, such as solar radiation, and therefore moderate the energy consumption of buildings. A parametric study was carried out on a switchable ethylene-tetrafluoroethylene (ETFE) foil cushion with the purpose of investigating the optical performance of an adaptive building envelope and its impact on building energy performance regarding heating, cooling and lighting. Ray-tracing techniques were used to investigate the effects of surface curvature, frit layout and frit properties, on the optical performance of the cushion in open and closed mode. A range of incidence angles for solar radiation were simulated. The results of the simulation showed an angle dependent optical behaviour for both modes. The influence of the dynamic shading mechanism on building energy performance was further evaluated by integrating the optical data obtained for the ETFE foil cushions in a comprehensive energy simulation of a generic atrium building using EnergyPlus. Results suggested that switchable ETFE foil cushions have a higher potential to reduce cooling and heating loads in different climatic regions, compared to conventional glazing solutions (i.e. uncoated double-glazing and reflective double-glazing), while providing good conditions of natural daylighting. Annual energy savings of up to 44.9% were predicted for the switchable ETFE foil cushion in comparison to reflective double glazing. As such, this study provides additional insight into the optical behaviour of multilayer foil constructions and the factors of design and environment that potentially have a major impact on buildings energy performance.

The development of nursing expertise is therefore vital in terms of progressing the nursing profession, primary care and substance misuse treatment services. This chapter outlines the key knowledge base that can inform the working of an addiction nurse in primary care. To expand this knowledge base requires a commitment to clinical supervision either individually or preferably in a multi-disciplinary group setting, particularly if the nurse is working autonomously and managed in a secondary care service elsewhere. Problems can emerge if there is conflict between the management of care between two or more services that may require resolution at a managerial policy making level in addition to good communication between clinicians. The chapter considers the impact of another key area of change on the delivery of substance misuse treatments, that of nurse prescribing. The introduction of the nurse consultant role has provided an unprecedented opportunity for the nursing profession and for individual nurses in the UK.

Tumours evolve through time and space. Computational techniques have been developed to infer their evolutionary dynamics from DNA sequencing data. A growing number of studies have used these approaches to link molecular cancer evolution to clinical progression and response to therapy. There has not yet been a systematic evaluation of methods for reconstructing tumour subclonality, in part due to the underlying mathematical and biological complexity and to difficulties in creating gold-standards. To fill this gap, we systematically elucidated the key algorithmic problems in subclonal reconstruction and developed mathematically valid quantitative metrics for evaluating them. We then created approaches to simulate realistic tumour genomes, harbouring all known mutation types and processes both clonally and subclonally. We then simulated 580 tumour genomes for reconstruction, varying tumour read-depth and benchmarking somatic variant detection and subclonal reconstruction strategies. The inference of tumour phylogenies is rapidly becoming standard practice in cancer genome analysis; this study creates a baseline for its evaluation.

Background:\ud \ud Dual diagnosis covers a broad spectrum of mental health and substance misuse conditions occurring concurrently (NICE, 2016). Its manifestation is complex and as such, the disorder is recognized as influencing adherence to prescribed medication, service engagement and has a worse prognosis than substance use and mental health conditions occurring independently.\ud \ud \ud Aims:\ud \ud To determine the effectiveness of psycho-educational group therapy on a sample of dual diagnosis patients.\ud \ud \ud Methods:\ud \ud Patients who met the DSM-IV Axis 1 criteria for serious mental illness and current substance misuse were approached to take part in a psycho-educational programme. Those who consented were assessed at baseline and end-point using measures of psychiatric symptomology, psychological well-being and substance use patterns with the following scales; Brief Psychiatric Rating Scale (BPRS), Hospital Anxiety and Depression Rating Scale (HADS), Maudsley Addiction Profile Scale (MAPS) and the Warwick and Edinburgh Mental Well-being Scale (WEMWBS).\ud \ud \ud Results:\ud \ud Fifty-one patients completed the programme whilst 29 dropped out after initial assessment. Between baseline and follow-up there was a decline in the number of participants using alcohol, cannabis, cocaine, amphetamine, illicit benzodiazepines and methadone. However, the number of participants using heroin remained constant. The mean amount of substances used did not reduce over the study period except in the case of alcohol. Overall improvements in symptomology and psychological well-being were observed.\ud \ud \ud Discussion:\ud \ud Mental health services should focus on integrated approaches via multimodal treatment interventions that encapsulate harm reduction and educational initiatives: Despite the modest sample, the findings have emphasized the importance of a broad range of treatment approaches delivered within a unitary delivery system.

The TensiNet Association, in collaboration with the COST Action TU1303 “Novel structural skins: Improving sustainability and efficiency through new structural textile materials and designs” and the Newcastle University organized the TensiNet - COST Action TU1303 Symposium 2016 held in Newcastle upon Tyne, UK, from Wednesday 26th to Friday 28th October 2016.This paper presents the 3-day event introducing the topics selected for the sessions, the keynote lectures and speakers and the sponsors which supported the organization of the symposium.

This paper presents the results of the field work on the luminous environment conducted in an atrium enclosed by an ethylene-tetra-fluoro-ethylene (ETFE) cushion roof and a test structure constructed with ETFE-encapsulated panels. In addition to the on-site monitoring, theoretical parametric studies using a scaled physical model of the ETFE panel structure were undertaken to further investigate the lit environment created by changing the transparency of the test structure envelope. The aim is to explore how the typical homogeneous and dull luminous environment can be improved. Subjective appreciation of the lit scenes and quantitative analysis results are compared and discussed. This study concluded that selective use of translucent and opaque components in the ETFE enclosures can offer opportunities to create well balanced, yet dynamic lighting conditions. Also selective positioning of these components in different parts of the ETFE structures can help improve modelling effect and enhance visual perception.

Summary Fueled by the radically increased capacity to generate data over the past decade, the field of biomedical research has been constrained by the ability to analyze data. Galaxy, a Web-based, open-source data integration and analysis platform for life science research, has been democratizing access to data analysis tools. However, the scale of data and the scope of tools required have proven to be a significant challenge for any monolithic deployment of the Galaxy application. We have found that a distributed and federated approach to utilizing compute and storage resources is necessary. This paper describes the ongoing efforts in creating a ubiquitous platform capable of simultaneously utilizing dedicated as well as on-demand cloud resources. Specifically, the requirements, process, and an implementation of a cloud-bursting system are detailed. Copyright © 2010 John Wiley & Sons, Ltd.

Many areas of research suffer from poor reproducibility, particularly in computationally intensive domains where results rely on a series of complex methodological decisions that are not well captured by traditional publication approaches. Various guidelines have emerged for achieving reproducibility, but implementation of these practices remains difficult due to the challenge of assembling software tools plus associated libraries, connecting tools together into pipelines, and specifying parameters. Here, we discuss a suite of cutting-edge technologies that make computational reproducibility not just possible, but practical in both time and effort. This suite combines three well-tested components—a system for building highly portable packages of bioinformatics software, containerization and virtualization technologies for isolating reusable execution environments for these packages, and workflow systems that automatically orchestrate the composition of these packages for entire pipelines—to achieve an unprecedented level of computational reproducibility. We also provide a practical implementation and five recommendations to help set a typical researcher on the path to performing data analyses reproducibly.

Reinforced concrete shells frequently constitute the most visible element of a building envelope. They dominate the architectural expression, yet the three-dimensional form is generally determined by the engineer according to its structural efficiency, rather than by the architect according to aesthetical considerations. This raises the question “Who is the author of the design?” The design philosophy of recognised shell designers is introduced, specifically that of Swiss shell designer and “structural artist” Heinz Isler, who is considered to have had particular sensitivity to the aesthetics of his shells, rooted in his admiration of the natural world and derived by natural laws. The Sicli Factory shell, 1968, is taken as a case study and is used to compare Isler’s design method with contemporary digital form-finding using the particle spring method. It is concluded that there are advantages and disadvantages to both physical and digital modelling methods. Designers should be encouraged to explore with various approaches.

The primary problem with the explosion of biomedical datasets is not the data itself, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web-browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences.

Membrane and foil structures have become over the last decades an attractive alternative to conventional materials and building systems with increasing implementation in different typologies and scale. The development of transparent, light, flexible and resistant materials like Ethylene Tetrafluoroethylene (ETFE) has triggered a rethinking of the building envelope in the building industry towards lightweight systems. ETFE foil cushions have proven to fulfil the design requirements in terms of structural efficiency and aesthetic values. But the strategies to satisfy increasing demands of energy efficiency and comfort conditions are still under development. The prediction and manipulation of the thermo-optical behaviour of ETFE foil cushion structures currently remain as one of the main challenges for designers and manufacturers. This paper reviews ongoing research regarding the control of the thermo-optical performance of ETFE cushion structures and highlights challenges and possible improvements. An overview of different dynamic and responsive environmental control mechanisms for multilayer foil constructions is provided and the state of the art in building application outlined by the discussion of case studies.

Hereditary congenital facial palsy (HCFP) is a rare congenital cranial dysinnervation disorder, recognisable by non-progressive isolated facial nerve palsy (cranial nerve VII). It is caused by developmental abnormalities of the facial nerve nucleus and its nerve. So far, 4 homozygous mutations have been identified in 5 unrelated families (12 patients) with HCFP worldwide. In this study, a large Iranian consanguineous kindred with 5 members affected by HCFP underwent thorough clinical and genetic evaluation. The candidate gene HOXB1 was screened and analysed by Sanger sequencing. As in previous cases, the most remarkable findings in the affected members of the family were mask-like faces, bilateral facial palsy with variable sensorineural hearing loss, and some dysmorphic features. Direct sequencing of the candidate gene HOXB1 identified a novel homozygous frameshift mutation (c.296_302del; p.Y99Wfs*20) which co-segregated with the disease phenotype within the extended family. Our findings expand the mutational spectrum of HOXB1 involved in HCFP and consolidate the role of the gene in the development of autosomal recessive HCFP. Moreover, the truncating mutation identified in this family leads to a broadly similar presentation and severity observed in previous patients with nonsense and missense mutations. This study characterises and defines the phenotypic features of this rare syndrome in a larger family than has previously been reported.

What does it take to convert a heap of sequencing data into a publishable result? First, common tools are employed to reduce primary data (sequencing reads) to a form suitable for further analyses (i.e., the list of variable sites). The subsequent exploratory stage is much more ad hoc and requires the development of custom scripts and pipelines, making it problematic for biomedical researchers. Here, we describe a hybrid platform combining common analysis pathways with the ability to explore data interactively. It aims to fully encompass and simplify the "raw data-to-publication" pathway and make it reproducible., Author summary Galaxy users can utilize a large number of tools and workflows. What they could not previously do is run ad hoc scripts and arbitrary tools within their Galaxy instance. This was very limiting, as initial analyses of data often involve interactive exploration with tools like Jupyter or RStudio—powerful platforms that are becoming increasingly popular in life sciences. Here, we showcase Galaxy Interactive Environment framework, designed to combine Galaxy's tools and workflows with environments such as Jupyter.

ETFE pneumatic foil constructions are used increasingly by designers and builders as an alternative to glass in state of the art building envelopes. Low weight, high transparency, mechanical resistance and self-cleaning properties of ETFE may contribute to the overall performance. However, reliable information on the thermal performance of ETFE cushions in building envelopes is scarce, limiting the performance prediction in energy simulations. The present study aims to investigate the thermal performance of air-inflated ETFE foil cushions and evaluates parameters of material properties and design which might affect the thermal transmittance. The paper reports on the experiments conducted to quantify the thermal performance using a climate chamber and full-size mock-ups. Based on available standards, tests were designed to compare the thermal performance of three different ETFE cushion designs, under changing climate conditions. The design variations, including frit prints and switchable shading mechanisms, were tested and compared at hot, temperate and cold weather scenarios. The test series provided detailed results on the thermal performance of ETFE cushions which may be of use for the comparison with the performance of other building components and materials, serve as input for energy simulations and provide a theoretical basis for future developments of novel building envelopes.

The fluoropolymer ethylene tetra-fluoro-ethylene (ETFE) in the form of thin foil is being used increasingly in architecture, in innovative building envelopes, either as a single-layer or, more commonly, as multi-layer inflated cushions. With foil thicknesses ranging from 100 to 300 µm, three-layer cushions typically weigh less than 1ṡ0 kg/m2. This paper reviews the main characteristics of ETFE foil that affect its use in architecture and discusses how developments in material technology and systems over the 30 years that the material has been used in permanent building envelopes have expanded the scope for architectural applications. Current state-of-the-art is illustrated through case studies of recently completed projects such as the north-light-like, multi-layer cushion, roof at the Dolce Vita Tejo shopping mall, Amadora, Portugal (2009); the external cushion cladding of the Media-TIC building, Barcelona (2010); and the single-layer façade of the Unilever Building in Hamburg (2009). It is concluded that there remain interesting possibilities for performance enhancement of ETFE foil-covered building envelopes that are able to adapt to provide desired thermal/optical performance as components in intelligent building skins and expand ETFE foil's fitness for use in more extreme climatic zones.

Groundwater is a key natural resource supporting socioeconomic development, but still quite widely misunderstood, undervalued, poorly managed and inadequately protected. Anthropogenic perturbation of groundwater systems accelerated markedly during the 20th century, as a result of massive exploitation for urban water-supply and irrigated agriculture, and radical land-use changes in many aquifer recharge zones. Increasing concerns about resource sustainability, quality degradation and dependent-ecosystem impacts have arisen, but despite notable technological advances it is not straightforward to provide a quantitative global assessment of groundwater status, given its widespread distribution, difficulty of aggregation and inadequate investment in monitoring. The challenge of identifying appropriate governance provisions and of translating these into effective institutional arrangements for local resource administration and quality protection is also considerable, but some successes have been recently achieved. An overview of resource assessment and management trends is presented in a form accessible to the broader environmental sector.

This paper presents an experimental approach to investigate the luminous environment in lightweight fabric structures through field study. Buildings selected for the field study included the Engineering Science Learning Centre at the University of Nottingham and the Clarke Quay in Singapore.By undertaking on site monitoring under different sky conditions in the chosen buildings with distinctively different site context, this research project explores how the typical homogeneously lit and rather dull luminous environment in lightweight fabric structure can be improved for enhanced visual interest, visual comfort, and three-dimensional modelling under both sunny and overcast sky conditions. Research data obtained from the subjective appreciation of the internal luminous environments and the quantitative spot measurement and mapping of light are compared and discussed.This study concluded that selective use of transparent and translucent components in the ETFE envelope can offer architectural designers the opportunities to create well balanced, yet dynamic lit scenes. Also by combining single skin ETFE foil and the double or triple layered ETFE cushion and introducing ETFE cushions with different light transmittance to the building envelope can help improve the overall visual and luminous environment and enhance task illumination. The key findings from this research work are applicable to the design of light in lightweight fabric structure in general.

What does it take to convert a heap of sequencing data into a publishable result? First, common tools are employed to reduce primary data (sequencing reads) to a form suitable for further analyses (i.e., list of variable sites). The subsequent exploratory stage is much moread hocand requires development of custom scripts making it problematic for biomedical researchers. Here we describe a hybrid platform combining common analysis pathways with exploratory environments. It aims at fully encompassing and simplifying the “raw data-to-publication” pathway and making it reproducible.

The thermal performance of a greenhouse can be greatly affected by the thermal and optical properties of its envelope system. In this study, a novel skin for greenhouse consisting of ethene-co-tetrafluoroethene (ETFE) membrane and Phase Change Material (PCM) RT28 has been developed and has also been experimentally investigated. The optical behaviour of the developed ETFE-Phase Change Material module sample is measured using a spectrometer and a pyranometer, respectively. The results show that at liquid state, the module has higher transmittance than that of at solid state. In addition, the light transmittance is related to the PCM's temperature. In the thermal aspect, the ETFE-Phase Change Material module presents different characterisation under various irradiances. Comparative analysis is also conducted for the ETFE-Phase Change Material, ETFE-water and ETFE alone. The ETFE-Phase Change Material system shows a benefit of the thermal management than that of other systems.

Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. The iRT of a peptide is a fixed number relative to a standard set of reference iRT-peptides that can be transferred across laboratories and chromatographic systems. We show that iRT facilitates the setup of multiplexed experiments with acquisition windows more than four times smaller compared to in silico RT predictions resulting in improved quantification accuracy. iRTs can be determined by any laboratory and shared transparently. The iRT concept has been implemented in Skyline, the most widely used software for MRM experiments.