Galaxy: A Decade of Realising CWFR Concepts

Despite recent encouragement to follow the FAIR principles, the day-to-day research practices have not changed substantially. Due to new developments and the increasing pressure to apply best practices, initiatives to improve the efficiency and reproducibility of scientific workflows are becoming more prevalent. In this article, we discuss the importance of well-annotated tools and the specific requirements to ensure reproducible research with FAIR outputs. We detail how Galaxy, an open-source workflow management system with a web-based interface, has implemented the concepts that are put forward by the Canonical Workflow Framework for Research (CWFR), whilst minimising changes to the practices of scientific communities. Although we showcase concrete applications from two different domains, this approach is generalisable to any domain and particularly useful in interdisciplinary research and science-based applications.publishedVersio

Framework to Automatically Determine the Quality of Open Data Catalogs

Data catalogs play a crucial role in modern data-driven organizations by facilitating the discovery, understanding, and utilization of diverse data assets. However, ensuring their quality and reliability is complex, especially in open and large-scale data environments. This paper proposes a framework to automatically determine the quality of open data catalogs, addressing the need for efficient and reliable quality assessment mechanisms. Our framework can analyze various core quality dimensions, such as accuracy, completeness, consistency, scalability, and timeliness, offer several alternatives for the assessment of compatibility and similarity across such catalogs as well as the implementation of a set of non-core quality dimensions such as provenance, readability, and licensing. The goal is to empower data-driven organizations to make informed decisions based on trustworthy and well-curated data assets. The source code that illustrates our approach can be downloaded from https://www.github.com/jorge-martinez-gil/dataq/.Comment: 25 page

Enabling Data-Driven Mobility Research: Design Principles and Design Features for an Open Platform Approach

In the field of mobility research, up-to-date data are needed in order to explore current problems and challenges. Proponents of Open Science argue that research data should be Findable, Accessible, Interoperable, and Reusable (FAIR). Adopting the Design Science Research methodology, we derive design requirements, design principles and design features for a suitable platform to realize the FAIR principles, based on a literature review, existing solutions, and interviews with mobility researchers (with qualitative and quantitative research backgrounds). In a practical way, and after an evaluation of our prototype, we show how a platform should be designed to allow users, regardless of their level of experience, to participate. We contribute to the discussion in the field of Open Science on how artifacts should be designed according to an open design, which also takes into account the different needs of researchers

Web Standards to Enable an Accessible and Inclusive Internet of Things (IoT)

The Internet of Things (IoT) is expected to have an unprecedented impact on our daily lives. In particular, “smart environments” will change how we interact with our surrounding and with each other, including at home, in public spaces, and at the work place. This provides an opportunity to ensure equal access for people with disabilities. For example, operating doors, windows, and physical objects through voice makes such environments more accessible to people with physical disabilities and inclusive to more. Yet there are still many challenges to address, without which the Internet of Things (IoT) threatens to be more of a disabler than an enabler. In particular, the current lack of interoperability makes it hard for assistive technologies to easily tap into IoT systems.Web standards could extend the open web platform to resolve many of these issues, much as it did on the traditional internet. This Web of Things (WoT) provides a robust application layer for innovation to thrive on the underlying Internet of Things (IoT). This paper outlines the relevance of IoT for people with disabilities and the specific challenges it currently poses. It then discusses how the Web of Things (WoT) could help address these challenges, and highlights research questions that still need to be tackled

How to Improve Accessibility of Natural Areas: About the Relevance of Providing Information on Accessible Services and Facilities in Natural Areas

Accessibility is a topic of increasing importance concerning all fields of life. This is underlined by current legislation as well as social meaning and economic benefits related to accessibility. Due to recent demographic changes in society characterised by steadily growing numbers of the elderly (with age-related physical deficits), enabling people with disabilities to manage their everyday independently gets even more important. However, in order to fully participate in life self-determined, the disabled demand for barrier free infrastructure in many ways. This is particularly true in terms of tourist and recreational activities in natural areas. At that, positive effects of being in nature (e.g. on people’s physical health and mental well-being as well as integration and family solidarity) are even more relevant for disabled people than for others. While many efforts exist on offering and improving barrier free services and facilities on-site, it seems that there is a lack of off-site material informing persons with disabilities of accessible services and facilities available in natural areas. That is surprising, since today, rapid advances in information and communication technologies offer many ways to provide digital, i.e. web-based solution suitable to impart all kinds of information and to meet the needs of disabled people. Concerning the spatial reference of nature-based recreation, i.e. in order to communicate location and spatial relationship of services and facilities, web-based maps are a central means of communication. But, which information regarding tourist and recreational visits of natural areas is required by disabled visitors? How to present this information to the target group in an accessible and useful way? How to design and integrate web-based maps as powerful tool to impart spatial information? Based on research conducted within the project “senTOUR”, this paper aims to offer suggestions for proving accessible digital information in order to support recreational and tourist activities in natural areas for disabled visitors, i.e. for the elderly who often suffer from age-related physical deficits

Available approaches to heuristic evaluation of smart-phone applications

Abstract. Usability heuristics are a lightweight tool for finding usability problems in a piece of software. These heuristics can be used for any kind of software, from desktop applications to web sites to games and to smart-phone applications. With the rise of smart phones and applications developed for them there has been a need to update the approach of heuristic evaluation to consider the limitations and new possibilities brought by smart-phone applications, when compared to more traditional desk-top applications. In this bachelor’s thesis different these issues are discussed, and along this several lists of usability heuristics were identified and listed. In addition to listing out the current research on smart-phone application heuristics, these lists were compared against the issues that are specific to smart-phone applications. Research questions in this thesis are as follows: RQ1: What guidelines / usability heuristics can be found that specifically target mobile device user interfaces? RQ2: How do these heuristic lists consider the difficulties faced by smart-phone applications

The challenges of data in future pandemics

This work was supported by Engineering and Physical Sciences Research Council (EPSRC) grant no. EP/R014604/1. M.C. was funded by the Engineering and Physical Sciences Research Council (EPSRC) grant no. EP/V054236/1. G.M. is supported by the Scottish Government’s Rural and Environment Science and Analytical Services Division (RESAS). J.P-G’s work is supported by funding from the UK Health Security Agency and the UK Department of Health and Social Care. L.P. is funded by the Wellcome Trust, UK and the Royal Society, UK (grant no. 202562/Z/16/Z). L.P. is supported by the UK Research and Innovation (UKRI) through the JUNIPER modelling consortium (grant no. MR/V038613/1). L.P. is also supported by The Alan Turing Institute for Data Science and Artificial Intelligence, UK. R.R was supported by the Natural Environment Research Council (NERC) grant no. NE/T004193/1 and NE/T010355/1, the Engineering and Physical Sciences Research Council (EPSRC) grant no. EP/V054236/1 and the Science and Technology Facilities Council (STFC) grant no. ST/V006126/1.The use of data has been essential throughout the unfolding COVID-19 pandemic. We have needed it to populate our models, inform our understanding, and shape our responses to the disease. However, data has not always been easy to find and access, it has varied in quality and coverage, been difficult to reuse or repurpose. This paper reviews these and other challenges and recommends steps to develop a data ecosystem better able to deal with future pandemics by better supporting preparedness, prevention, detection and response.Publisher PDFPeer reviewe

Toward a Standardized Strategy of Clinical Metabolomics for the Advancement of Precision Medicine

Despite the tremendous success, pitfalls have been observed in every step of a clinical metabolomics workflow, which impedes the internal validity of the study. Furthermore, the demand for logistics, instrumentations, and computational resources for metabolic phenotyping studies has far exceeded our expectations. In this conceptual review, we will cover inclusive barriers of a metabolomics-based clinical study and suggest potential solutions in the hope of enhancing study robustness, usability, and transferability. The importance of quality assurance and quality control procedures is discussed, followed by a practical rule containing five phases, including two additional "pre-pre-" and "post-post-" analytical steps. Besides, we will elucidate the potential involvement of machine learning and demonstrate that the need for automated data mining algorithms to improve the quality of future research is undeniable. Consequently, we propose a comprehensive metabolomics framework, along with an appropriate checklist refined from current guidelines and our previously published assessment, in the attempt to accurately translate achievements in metabolomics into clinical and epidemiological research. Furthermore, the integration of multifaceted multi-omics approaches with metabolomics as the pillar member is in urgent need. When combining with other social or nutritional factors, we can gather complete omics profiles for a particular disease. Our discussion reflects the current obstacles and potential solutions toward the progressing trend of utilizing metabolomics in clinical research to create the next-generation healthcare system.11Ysciescopu

CWLProv - Interoperable Retrospective Provenance capture and its challenges

<p>The automation of data analysis in the form of scientific workflows is a widely adopted practice in many fields of research nowadays. Computationally driven data-intensive experiments using workflows enable <strong>A</strong>utomation, <strong>S</strong>caling, <strong>A</strong>daption and <strong>P</strong>rovenance support (ASAP).</p> <p>However, there are still several challenges associated with the effective sharing, publication, understandability and reproducibility of such workflows due to the incomplete capture of provenance and the dependence on particular technical (software) platforms. This paper presents <strong>CWLProv</strong>, an approach for retrospective provenance capture utilizing open source community-driven standards involving application and customization of workflow-centric <a href="http://www.researchobject.org/">Research Objects</a> (ROs).</p> <p>The ROs are produced as an output of a workflow enactment defined in the <a href="http://www.commonwl.org/">Common Workflow Language</a> (CWL) using the CWL reference implementation and its data structures. The approach aggregates and annotates all the resources involved in the scientific investigation including inputs, outputs, workflow specification, command line tool specifications and input parameter settings. The resources are linked within the RO to enable re-enactment of an analysis without depending on external resources.</p> <p>The workflow provenance profile is represented in W3C recommended standard <a href="https://www.w3.org/TR/prov-n/">PROV-N</a> and <a href="https://www.w3.org/Submission/prov-json/">PROV-JSON</a> format to capture retrospective provenance of the workflow enactment. The workflow-centric RO produced as an output of a CWL workflow enactment is expected to be interoperable, reusable, shareable and portable across different plat-<br> forms.</p> <p>This paper describes the need and motivation for <a href="https://github.com/common-workflow-language/cwltool/tree/provenance">CWLProv</a> and the lessons learned in applying it for ROs using CWL in the bioinformatics domain.</p