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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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.