The number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available and reproducible. To demonstrate its utility, we reanalysed 10 public DIA datasets from the PRIDE database, comprising 1,278 SWATH-MS runs. The robustness of the analysis was evaluated, and the results compared to those obtained in the original publications. The final expression values were integrated into Expression Atlas, making SWATH-MS experiments more widely available and combining them with expression data originating from other proteomics and transcriptomics datasets.

1 Department of Computer Science, The University of Manchester, Manchester, United Kingdom, 2 Melandra Limited, Stockport, United Kingdom, 3 Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands, 4 Research IT, IT Services, University of Manchester, Manchester, United Kingdom, 5 Meise Botanic Garden, Meise, Belgium, 6 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium, 7 VIB Center for Plant Systems Biology, Ghent, Belgium, 8 Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany, 9 Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden

Software developers use version control systems for collaborative coding. These systems are integrated into several software development platforms (including GitLab and GitHub) which support additional software engineering functionalities. Using these platforms in an educational context allows students to gain skills relevant to industry, whilst providing a means of keeping track of their activities. In this paper, we investigate the effect of presenting teams of students with GitLab metrics about their performance at coursework consultation sessions (checkpoint sessions), with a particular focus on the number of issues assigned and completed, and the number of commits made to the repository. A comparative analysis of project marks in two consecutive academic years indicates that these checkpoint sessions may lead to better student outcomes. An interview study with students and teaching assistants identified viewing the GitLab metrics in the checkpoints as an opportunity to see the relative contributions of team members and address resulting issues, and as a catalyst for improving engagement with the team project. The study also identified drawbacks of using the metrics too simplistically, and suggested that it was important to consider the quality and amount of written code, as well as the number of times someone committed to the repository. (C) 2020 Elsevier Inc. All rights reserved.

이 글은 방송분야에서의 콘텐츠 접근에 관한 EU 경쟁법과 정책, 그리고 몇 가지 규제적 측면들을 검토하고 있다. 이 글은 먼저 콘텐츠 생성, 프로그램방송권(program rights)의 도매판매, 채널 패키징, 전달 또는 전송, 수익 창출 또는 소매판매로 구성되는 가치사슬 내에서 방송 콘텐츠의 위치를 설정한다. 이러한 구조적 틀 안에서 콘텐츠와 관련하여 두 종류의 경쟁법적 문제가 발생한다. 하나는 콘텐츠 생성 및 /또는 프로그램 도매시장의 독점화 문제이고 다른 하나는 프로그램 도매판매와 전달체계 사이의 (양쪽방향 모두) 시장지배력 전이(leveraging)의 문제이다. 유럽의 방송시장 분석의 출발점은 시장획정이다. 이 글은 유럽에서 다뤄진 경쟁법 사건들 중 프로그램 방송권과 관련하여 제기된 시장획정의 문제를 검토한다. 이러한 사건들에서 스포츠 방송권은, 보다 엄밀히 말하면 축구경기 방송권은 별개의 독립된 시장으로 정의된 바 있다. 유료방송 콘텐츠와 무료방송 콘텐츠 사이의 관계 역시 중요하다. 많은 유럽의 경쟁법 사건들은 스포츠 리그 클럽들의 방송권 일괄판매(collective selling)를 다루고 있다. 경쟁당국의 역할을 하는 유럽집행위원회는 방송판매기간을 제한하고, 방송권을 여러 개의 패키지로 분할하여 판매하게 하는 등 그러한 방송권의 판매행위에 대하여 다양한 규제를 해왔다. 할리우드 영화제작사들이 판매하는 영화방영권에 대해서도 다양한 규제를 하고 있다. 영국의 경우, 경쟁당국이 유료TV방송 지배사업자가 부과하는 소매가격과 동 사업자가 소매 경쟁사업자에게 부과하는 프로그램 도매가격 간의 가격 압착의 가능성을 조사하였다. 영국 경쟁당국은 분석을 위하여 개념상 방송사업자의 도매활동과 유통회사를 구별하였다. 분석결과는 경계선상에 위치하였으며, 당국은 남용을 입증할 만한 충분한 근거를 제시하지 못했다. 유럽에서는 유료TV방송사업자들의 기업결합의 조건으로 국가경쟁당국이나 유럽집행위원회가 결합된 방송사업자에게 대개는 다른 플랫폼 사업자인 실제 또는 잠재적 소매경쟁사업자에게 프로그램을 제공하도록 하고 있다. 이 경우 가격문제가 핵심문제이며, 가격에 대한 대안적 접근방법은 원가기반요금산정방식(cost-based prices), 소매요금 차감방식(retail minus prices) 그리고 협상에 근거한 방식 등이 있다. 대개는 분쟁해결절차가 사용된다. 이 글은 또한 영국의 규제당국이 유료TV방송 지배사업자에게 특정 프리미엄 스포츠 채널에 대한 접근을 소매경쟁사업자에게 허용하도록 한 현행 규제에 대하여 제기된 소송에 관한 배경설명도 포함하고 있다. 마지막으로, 유럽공동체의 규제방식은 적법한 공익을 목적으로 콘텐츠의 보편적 접근을 가능하도록 하기 위하여 전송서비스제공사업자에게 특정 채널을 전송할 의무를 부과할 수 있다. 이를 의무전송규칙(must-carry rules)이라고 한다. 방송사업자(일반적으로 공역무 방송사업자)에게 다른 플랫폼에 채널을 제공하도록 하는 의무제공규칙(must-offer rules)은 덜 일반적이다. 요컨대, 유럽의 방송 영역에서 가장 주요한 경쟁법적 현안은 방송권의 일괄판매와 도매시장의 지배사업자가 소유한 프로그램에 대한 의무적 접근의 문제이다. 그러나 비디오 콘텐츠 산업은 급변하고 있기 때문에 머지않아 새로운 쟁점들이 출현하게 될 것이다.

Epidemiology requires large-scale, high-resolution, representative population data sets; data extracted from electronic health record systems meets these criteria. However, within the UK, there is no single electronic health record, and the record of a patient's healthcare is fragmented over multiple systems and multiple organizations. In the SHORE project we have developed a proof of concept system that addresses these problems by retaining control of patient data at a local level, where it can be effectively interpreted and governed, and by overlaying on these data sources privacy-preserving record linkage providing a unified view of the health and care of the population.

The study of the genetics of diseases has been revolutionised by the advent of genome-wide genotyping technologies. Increasingly, genome-wide association studies are being used to identify positions within the human genome that have a link with a disease condition. These new data sets require the use of distributed resources, both for the statistical analysis and for the interpretation of the analysis results. Aiding the latter will be be crucial for the statistical analysis process to be successful. In this paper we report our experiences in developing a user-friendly High Performance Computing (HPC) statistical genetics analysis platform for use by clinical researchers. Specifically, we report work on supporting the interpretation process through the automatic annotation of the statistical analysis results with relevant biological information. Retrieval of the biological annotation is performed by high-volume invocation of multiple Web-services orchestrated via pre-existing scientific workflows. We also report work on developing tools to aid the capture and replay of the processes performed by a user when exploring analysis results.

GRAIL is a semantically constrained, generative compositional descriptive logic with subsumption and multiple inheritance designed to cope with the scale, complexity and variable granularity of medical concepts. It effectively represents a medical vocabulary for any application such as decision support systems, hospital record systems, clinical workstations and bibliographic systems. The EU-funded GALEN project aims to create a multilingual Terminology Server capable of being used as a resource by any medical application. The Terminology Server relates descriptive medical concepts represented in GRAIL to their natural language terms in a number of European languages and to corresponding (or best match) codes in conventional clinical coding schemes. In this paper we present GRAIL, the GALEN Terminology Server and make some remarks on the coupling of the classification-based clinical knowledge base (implemented in Smalltalk) with a relational database (Sybase).

To accurately support a patient's medical record, at least four interrelated models are required: a simple static one-level schema is inadequate. The models must support the medical record as a coherent story reconstructed from the sequence of recorded events within the medical record. We propose one representation which unifies all four models by a three space approach, each space acting as a schema for the space below. The three spaces assist atemporal summarisation of a patient's medical record and illustrate the difficulties of recording retrospective or contradictory observations. The approach uses a generative, descriptive subsumption-based classification formalism with a sophisticated system of semantic constraints controlling the generation of implied intensional concepts. We report our experiences in its use in a prototype clinical workstation. We believe that this model can be used for complex applications where contradictory and incomplete information is captured over time and a complex semantic constraint model is required.

The policy imperative to increase public participation in health and social care research, planning and service delivery raises significant questions about optimum approaches, methods and the extent to which this policy can influence change in practice. This paper highlights the key policy literature on user involvement and participatory research methods to establish the context for a partnership research project exploring perceptions of risk in relation to falls from the perspectives of older people, carers, and health and social care professionals. The paper reports the methods used in developing user involvement in the research at a number of levels, including project management, and a consumer panel working alongside the research team and influencing the dissemination in local falls prevention strategies. The authors draw out the issues related to the context and method of involvement, and discuss the impact on research quality and local service development in health and social care.

In this paper, we present a software tool that implements a novel modelling framework developed by the authors to provide useful information to budget planners for long-term care at local authority level. By combining unit costs of care with an underlying survival model for publicly funded residents in long-term care, the software tool is able to provide forecasts on the cost of maintaining the group of elderly who are currently in long-term care (referred to as known commitments) for a period of time. User interacts with the tool via a friendly graphical interface that guides them through a set of screens of options in a familiar wizard fashion. This tool was created and tested in collaboration with an English borough. Feedbacks from the care planner and manager show that the tool helps them gain better understanding on the behaviour of length-of-stay of residents under their care, and provides quantitative inputs into their decision making on budget planning for long-term care.

A Multimedia Information System (MMIS) is a repository for all types of electronically representable data (O’Docherty et al., 1990). Conventional databases provide a large set of operations for retrieval of simple data types. The simplest way of extending this to multimedia objects is to store and retrieve on the basis of a few manually entered associated attributes or links. The true potential of multimedia databases is realised when a rich set of operations is provided to allow transparent manipulation of data objects of all media. This can best be achieved through content retrieval, based on the automatic interpretation of medium objects. Automatic content retrieval avoids the problems of inconsistency, subjectivity and the labour-intensiveness of manual entry. MMISs with content retrieval will have wide application in industry, medicine, education and the military. The Multimedia Group at Manchester University have prototyped a MMIS for the content retrieval of images in a specific application domain and are developing a second system that includes content retrieval of text and documents. Hereafter, the term instance is used to refer to medium objects that are intended for interpretation in our system.

The terms Hidden Web, Deep Web and Invisible Web describe those resources on the Web that are in some way unreachable by search engines, and are potentially unusable to other Web systems such as annotation services. These hidden resources make up a significant part of the current Web. We provide firm definitions of the ways in which information can be “hidden”, and discuss the challenges that face those working with annotation in the Hidden Web. We do not attempt to provide solutions for these challenges, but a clarification of the terms involved is certainly a step in the right direction. Copyright c © 2004, University of Manchester. All rights reserved. Reproduction (electronically or by other means) of all or part of this work is permitted for educational or research purposes only, on condition that no commercial gain is involved. Recent preprints issued by the Department of Computer Science, Manchester University, are available on WWW via URL http://www.cs.man.ac.uk/preprints/index.html or by ftp from ftp.cs.man.ac.uk in the directory pub/preprints. Melandra Limited, Greenheys Centre, 10 Pencroft Way, Manchester, M15 6JJ Sun Microsystems Laboratories Europe, Sun Microsystems Ltd, Sun House, 306 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG

This document describes a simple API for a general description logic system. This forms the first of a number of such specifications. Later versions will introduce more higher-level functionality. The current, Level 0 specification provides basic access to the reasoning capabilities of a DL reasoner.

Geology TodayVolume 13, Issue 1 p. 7-19 News & Coment Geodigest Peter Crowther, Peter Crowther The Ulster Museum, BelfastSearch for more papers by this authorMike Simms, Mike Simms The Ulster Museum, BelfastSearch for more papers by this author Peter Crowther, Peter Crowther The Ulster Museum, BelfastSearch for more papers by this authorMike Simms, Mike Simms The Ulster Museum, BelfastSearch for more papers by this author First published: 30 October 2003 https://doi.org/10.1046/j.1365-2451.1997.d01-376.xCitations: 1AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume13, Issue1January 1997Pages 7-19 RelatedInformation

Traditional databases use simple data types chiefly numbers and strings—to represent information such as payroll records or scientific data. Queries commonly take the form of relational calculus or relational algebra expressions and the results require little more than a textual terminal for presen tation. The natural successor to a traditional database is the Multimedia Information System which also uses richer data types—images, text, sound and so on—to describe some application domain. This calls for more advanced technologies such as graphical workstations for data creation and presentation, high-bandwidth networks for fast access to distributed data and large repositories for the storage of objects. These technologies are now widely available. Ideally, queries put to a Multimedia Information System should refer to the content of stored objects—content retrieval—and results should be able to contain complex as well as simple data types. Manual entry of content descriptions is time-consuming, error-prone and subjective; a better approach is to draw on the emerging fields of image interpretation, text interpretation, speech interpretation and knowledge representation to provide automatic content retrieval. This article serves as an introduction to Multimedia Information Systems and related fields and describes in detail a pilot system with automatic content retrieval built by the Multimedia Group at Manchester University.