Reuse remix recycle: repurposing archaeological digital data

Preservation of digital data is predicated on the expectation of its reuse, yet that expectation has never been examined within archaeology. While we have extensive digital archives equipped to share data, evidence of reuse seems paradoxically limited. Most archaeological discussions have focused on data management and preservation and on disciplinary practices surrounding archiving and sharing data. This article addresses the reuse side of the data equation through a series of linked questions: What is the evidence for reuse, what constitutes reuse, what are the motivations for reuse, and what makes some data more suitable for reuse than others? It concludes by posing a series of questions aimed at better understanding our digital engagement with archaeological data

Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples

Report on the Second Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2)

This technical report records and discusses the Second Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2). The report includes a description of the alternative, experimental submission and review process, two workshop keynote presentations, a series of lightning talks, a discussion on sustainability, and five discussions from the topic areas of exploring sustainability; software development experiences; credit & incentives; reproducibility & reuse & sharing; and code testing & code review. For each topic, the report includes a list of tangible actions that were proposed and that would lead to potential change. The workshop recognized that reliance on scientific software is pervasive in all areas of world-leading research today. The workshop participants then proceeded to explore different perspectives on the concept of sustainability. Key enablers and barriers of sustainable scientific software were identified from their experiences. In addition, recommendations with new requirements such as software credit files and software prize frameworks were outlined for improving practices in sustainable software engineering. There was also broad consensus that formal training in software development or engineering was rare among the practitioners. Significant strides need to be made in building a sense of community via training in software and technical practices, on increasing their size and scope, and on better integrating them directly into graduate education programs. Finally, journals can define and publish policies to improve reproducibility, whereas reviewers can insist that authors provide sufficient information and access to data and software to allow them reproduce the results in the paper. Hence a list of criteria is compiled for journals to provide to reviewers so as to make it easier to review software submitted for publication as a “Software Paper.

Theory and Practice of Data Citation

Citations are the cornerstone of knowledge propagation and the primary means of assessing the quality of research, as well as directing investments in science. Science is increasingly becoming "data-intensive", where large volumes of data are collected and analyzed to discover complex patterns through simulations and experiments, and most scientific reference works have been replaced by online curated datasets. Yet, given a dataset, there is no quantitative, consistent and established way of knowing how it has been used over time, who contributed to its curation, what results have been yielded or what value it has. The development of a theory and practice of data citation is fundamental for considering data as first-class research objects with the same relevance and centrality of traditional scientific products. Many works in recent years have discussed data citation from different viewpoints: illustrating why data citation is needed, defining the principles and outlining recommendations for data citation systems, and providing computational methods for addressing specific issues of data citation. The current panorama is many-faceted and an overall view that brings together diverse aspects of this topic is still missing. Therefore, this paper aims to describe the lay of the land for data citation, both from the theoretical (the why and what) and the practical (the how) angle.Comment: 24 pages, 2 tables, pre-print accepted in Journal of the Association for Information Science and Technology (JASIST), 201

Chemical information matters: an e-Research perspective on information and data sharing in the chemical sciences

Recently, a number of organisations have called for open access to scientific information and especially to the data obtained from publicly funded research, among which the Royal Society report and the European Commission press release are particularly notable. It has long been accepted that building research on the foundations laid by other scientists is both effective and efficient. Regrettably, some disciplines, chemistry being one, have been slow to recognise the value of sharing and have thus been reluctant to curate their data and information in preparation for exchanging it. The very significant increases in both the volume and the complexity of the datasets produced has encouraged the expansion of e-Research, and stimulated the development of methodologies for managing, organising, and analysing "big data". We review the evolution of cheminformatics, the amalgam of chemistry, computer science, and information technology, and assess the wider e-Science and e-Research perspective. Chemical information does matter, as do matters of communicating data and collaborating with data. For chemistry, unique identifiers, structure representations, and property descriptors are essential to the activities of sharing and exchange. Open science entails the sharing of more than mere facts: for example, the publication of negative outcomes can facilitate better understanding of which synthetic routes to choose, an aspiration of the Dial-a-Molecule Grand Challenge. The protagonists of open notebook science go even further and exchange their thoughts and plans. We consider the concepts of preservation, curation, provenance, discovery, and access in the context of the research lifecycle, and then focus on the role of metadata, particularly the ontologies on which the emerging chemical Semantic Web will depend. Among our conclusions, we present our choice of the "grand challenges" for the preservation and sharing of chemical information

Dynamic Data Citation Service-Subset Tool for Operational Data Management

In earth observation and climatological sciences, data and their data services grow on a daily basis in a large spatial extent due to the high coverage rate of satellite sensors, model calculations, but also by continuous meteorological in situ observations. In order to reuse such data, especially data fragments as well as their data services in a collaborative and reproducible manner by citing the origin source, data analysts, e.g., researchers or impact modelers, need a possibility to identify the exact version, precise time information, parameter, and names of the dataset used. A manual process would make the citation of data fragments as a subset of an entire dataset rather complex and imprecise to obtain. Data in climate research are in most cases multidimensional, structured grid data that can change partially over time. The citation of such evolving content requires the approach of "dynamic data citation". The applied approach is based on associating queries with persistent identifiers. These queries contain the subsetting parameters, e.g., the spatial coordinates of the desired study area or the time frame with a start and end date, which are automatically included in the metadata of the newly generated subset and thus represent the information about the data history, the data provenance, which has to be established in data repository ecosystems. The Research Data Alliance Data Citation Working Group (RDA Data Citation WG) summarized the scientific status quo as well as the state of the art from existing citation and data management concepts and developed the scalable dynamic data citation methodology of evolving data. The Data Centre at the Climate Change Centre Austria (CCCA) has implemented the given recommendations and offers since 2017 an operational service on dynamic data citation on climate scenario data. With the consciousness that the objective of this topic brings a lot of dependencies on bibliographic citation research which is still under discussion, the CCCA service on Dynamic Data Citation focused on the climate domain specific issues, like characteristics of data, formats, software environment, and usage behavior. The current effort beyond spreading made experiences will be the scalability of the implementation, e.g., towards the potential of an Open Data Cube solution

Forschungssoftware in Bibliotheken

Software is increasingly acknowledged as valid research output. Academic libraries adapt to this change to become research software-ready. Software publication and citation are key areas in this endeavor. We present and discuss the current state of the practice of software publication and software citation, and discuss four areas of activity that libraries engage in: (1) technical infrastructure, (2) training and support, (3) software management and curation, (4) policies.Software wird zunehmend als gültiges Forschungsergebnis anerkannt. Wissenschaftliche Bibliotheken passen sich diesem Wandel an, um für Forschungssoftware gerüstet zu sein. Softwarepublikation und -zitierung sind hierbei Schlüsselbereiche. Wir präsentieren und diskutieren hier den aktuellen Praxisstand und heben vier Bereiche hervor, in denen Bibliotheken aktiv werden können, um für Forschungssoftware gerüstet zu sein: (1) technische Infrastruktur, (2) Schulung und Support, (3) Management und Kuratierung von Software, (4) Richtlinien.Peer Reviewe

Modeling domain metadata beyond metadata standards

The Laser Interferometer Gravitational-wave Observatory (LIGO) project to detect gravitational waves represents a complex, distributed scientific endeavor posing specific challenges for reproducibility and data management. The integration of provenance and other metadata information into the workflow stands as one means of addressing such challenges. The goal of a metadata model for the LIGO workflow is the provision of metadata describing all the data products at each significant milestone in the data analysis pipeline. Given both the highly specific domain and the need to support current analysis tools, the development of such a model demands a more complex, comprehensive approach. For this reason, we pursued a multipronged approach to metadata modeling, gathering users’ conceptions, system information, research artifacts, and other organizational documents, and worked to combine the findings into one final model. This approach provided a thorough understanding of the overall research lifecycle and insight into scientific workflow metadata modeling