Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv

Background: The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research. Computationally driven data-intensive experiments using workflows enable Automation, Scaling, Adaption and Provenance support (ASAP). However, there are still several challenges associated with the effective sharing, publication and reproducibility of such workflows due to the incomplete capture of provenance and lack of interoperability between different technical (software) platforms. Results: Based on best practice recommendations identified from literature on workflow design, sharing and publishing, we define a hierarchical provenance framework to achieve uniformity in the provenance and support comprehensive and fully re-executable workflows equipped with domain-specific information. To realise this framework, we present CWLProv, a standard-based format to represent any workflow-based computational analysis to produce workflow output artefacts that satisfy the various levels of provenance. We utilise open source community-driven standards; interoperable workflow definitions in Common Workflow Language (CWL), structured provenance representation using the W3C PROV model, and resource aggregation and sharing as workflow-centric Research Objects (RO) generated along with the final outputs of a given workflow enactment. We demonstrate the utility of this approach through a practical implementation of CWLProv and evaluation using real-life genomic workflows developed by independent groups. Conclusions: The underlying principles of the standards utilised by CWLProv enable semantically-rich and executable Research Objects that capture computational workflows with retrospective provenance such that any platform supporting CWL will be able to understand the analysis, re-use the methods for partial re-runs, or reproduce the analysis to validate the published findings.Submitted to GigaScience (GIGA-D-18-00483

Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation

BACKGROUND: Electronic Laboratory Notebooks (ELNs) are used to document experiments and investigations in the wet-lab. Protocols in ELNs contain a detailed description of the conducted steps including the necessary information to understand the procedure and the raised research data as well as to reproduce the research investigation. The purpose of this study is to investigate whether such ELN protocols can be used to create semantic documentation of the provenance of research data by the use of ontologies and linked data methodologies. METHODS: Based on an ELN protocol of a biomedical wet-lab experiment, a retrospective provenance model of the raised research data describing the details of the experiment in a machine-interpretable way is manually engineered. Furthermore, an automated approach for knowledge acquisition from ELN protocols is derived from these results. This structure-based approach exploits the structure in the experiment’s description such as headings, tables, and links, to translate the ELN protocol into a semantic knowledge representation. To satisfy the Findable, Accessible, Interoperable, and Reuseable (FAIR) guiding principles, a ready-to-publish bundle is created that contains the research data together with their semantic documentation. RESULTS: While the manual modelling efforts serve as proof of concept by employing one protocol, the automated structure-based approach demonstrates the potential generalisation with seven ELN protocols. For each of those protocols, a ready-to-publish bundle is created and, by employing the SPARQL query language, it is illustrated that questions about the processes and the obtained research data can be answered. CONCLUSIONS: The semantic documentation of research data obtained from the ELN protocols allows for the representation of the retrospective provenance of research data in a machine-interpretable way. Research Object Crate (RO-Crate) bundles including these models enable researchers to easily share the research data including the corresponding documentation, but also to search and relate the experiment to each other

The rockerverse : packages and applications for containerisation with R

The Rocker Project provides widely used Docker images for R across different application scenarios. This article surveys downstream projects that build upon the Rocker Project images and presents the current state of R packages for managing Docker images and controlling containers. These use cases cover diverse topics such as package development, reproducible research, collaborative work, cloud-based data processing, and production deployment of services. The variety of applications demonstrates the power of the Rocker Project specifically and containerisation in general. Across the diverse ways to use containers, we identified common themes: reproducible environments, scalability and efficiency, and portability across clouds. We conclude that the current growth and diversification of use cases is likely to continue its positive impact, but see the need for consolidating the Rockerverse ecosystem of packages, developing common practices for applications, and exploring alternative containerisation software

Scholarly Communication Librarianship and Open Knowledge

The intersection of scholarly communication librarianship and open education offers a unique opportunity to expand knowledge of scholarly communication topics in both education and practice. Open resources can address the gap in teaching timely and critical scholarly communication topics—copyright in teaching and research environments, academic publishing, emerging modes of scholarship, impact measurement—while increasing access to resources and equitable participation in education and scholarly communication. Scholarly Communication Librarianship and Open Knowledge is an open textbook and practitioner’s guide that collects theory, practice, and case studies from nearly 80 experts in scholarly communication and open education. Divided into three parts: *What is Scholarly Communication? *Scholarly Communication and Open Culture *Voices from the Field: Perspectives, Intersections, and Case Studies The book delves into the economic, social, policy, and legal aspects of scholarly communication as well as open access, open data, open education, and open science and infrastructure. Practitioners provide insight into the relationship between university presses and academic libraries, defining collection development as operational scholarly communication, and promotion and tenure and the challenge for open access. Scholarly Communication Librarianship and Open Knowledge is a thorough guide meant to increase instruction on scholarly communication and open education issues and practices so library workers can continue to meet the changing needs of students and faculty. It is also a political statement about the future to which we aspire and a challenge to the industrial, commercial, capitalistic tendencies encroaching on higher education. Students, readers, educators, and adaptors of this resource can find and embrace these themes throughout the text and embody them in their work

Building information modeling – A game changer for interoperability and a chance for digital preservation of architectural data?

Digital data associated with the architectural design-andconstruction process is an essential resource alongside -and even past- the lifecycle of the construction object it describes. Despite this, digital architectural data remains to be largely neglected in digital preservation research – and vice versa, digital preservation is so far neglected in the design-and-construction process. In the last 5 years, Building Information Modeling (BIM) has seen a growing adoption in the architecture and construction domains, marking a large step towards much needed interoperability. The open standard IFC (Industry Foundation Classes) is one way in which data is exchanged in BIM processes. This paper presents a first digital preservation based look at BIM processes, highlighting the history and adoption of the methods as well as the open file format standard IFC (Industry Foundation Classes) as one way to store and preserve BIM data