Repository of NSF Funded Publications and Data Sets: "Back of Envelope" 15 year Cost Estimate

In this back of envelope study we calculate the 15 year fixed and variable costs of setting up and running a data repository (or database) to store and serve the publications and datasets derived from research funded by the National Science Foundation (NSF). Costs are computed on a yearly basis using a fixed estimate of the number of papers that are published each year that list NSF as their funding agency. We assume each paper has one dataset and estimate the size of that dataset based on experience. By our estimates, the number of papers generated each year is 64,340. The average dataset size over all seven directorates of NSF is 32 gigabytes (GB). A total amount of data added to the repository is two petabytes (PB) per year, or 30 PB over 15 years. The architecture of the data/paper repository is based on a hierarchical storage model that uses a combination of fast disk for rapid access and tape for high reliability and cost efficient long-term storage. Data are ingested through workflows that are used in university institutional repositories, which add metadata and ensure data integrity. Average fixed costs is approximately $.0.90/GB over 15-year span. Variable costs are estimated at a sliding scale of$150 - $100 per new dataset for up-front curation, or$4.87 – $3.22 per GB. Variable costs reflect a 3 The total projected cost of the data and paper repository is estimated at$167,000,000 over 15 years of operation, curating close to one million of datasets and one million papers. After 15 years and 30 PB of data accumulated and curated, we estimate the cost per gigabyte at $5.56. This$167 million cost is a direct cost in that it does not include federally allowable indirect costs return (ICR). After 15 years, it is reasonable to assume that some datasets will be compressed and rarely accessed. Others may be deemed no longer valuable, e.g., because they are replaced by more accurate results. Therefore, at some point the data growth in the repository will need to be adjusted by use of strategic preservation

Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices

Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems, a diverse array of biological systems have been the target of large-scale computational modeling efforts. Nonetheless, these research agendas have yet to prove decisively their value among the broader community of theoretical and experimental biologists. In this commentary, we examine a range of philosophical and practical issues relevant to understanding the potential of integrative simulations. We discuss the role of theory and modeling in different areas of physics and suggest that certain sub-disciplines of physics provide useful cultural analogies for imagining the future role of simulations in biological research. We examine philosophical issues related to modeling which consistently arise in discussions about integrative simulations and suggest a pragmatic viewpoint that balances a belief in philosophy with the recognition of the relative infancy of our state of philosophical understanding. Finally, we discuss community workflow and publication practices to allow research to be readily discoverable and amenable to incorporation into simulations. We argue that there are aligned incentives in widespread adoption of practices which will both advance the needs of integrative simulation efforts as well as other contemporary trends in the biological sciences, ranging from open science and data sharing to improving reproducibility.Comment: 10 page

An Exploratory Sequential Mixed Methods Approach to Understanding Researchers’ Data Management Practices at UVM: Integrated Findings to Develop Research Data Services

This article reports on the integrated findings of an exploratory sequential mixed methods research design aimed to understand data management behaviors and challenges of faculty at the University of Vermont (UVM) in order to develop relevant research data services. The exploratory sequential mixed methods design is characterized by an initial qualitative phase of data collection and analysis, followed by a phase of quantitative data collection and analysis, with a final phase of integration or linking of data from the two separate strands of data. A joint display was used to integrate data focused on the three primary research questions: How do faculty at UVM manage their research data, in particular how do they share and preserve data in the long-term?; What challenges or barriers do UVM faculty face in effectively managing their research data?; and What institutional data management support or services are UVM faculty interested in? As a result of the analysis, this study suggests four major areas of research data services for UVM to address: infrastructure, metadata, data analysis and statistical support, and informational research data services. The implementation of these potential areas of research data services is underscored by the need for cross-campus collaboration and support

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

Making open data work for plant scientists

Despite the clear demand for open data sharing, its implementation within plant science is still limited. This is, at least in part, because open data-sharing raises several unanswered questions and challenges to current research practices. In this commentary, some of the challenges encountered by plant researchers at the bench when generating, interpreting, and attempting to disseminate their data have been highlighted. The difficulties involved in sharing sequencing, transcriptomics, proteomics, and metabolomics data are reviewed. The benefits and drawbacks of three data-sharing venues currently available to plant scientists are identified and assessed: (i) journal publication; (ii) university repositories; and (iii) community and project-specific databases. It is concluded that community and project-specific databases are the most useful to researchers interested in effective data sharing, since these databases are explicitly created to meet the researchers’ needs, support extensive curation, and embody a heightened awareness of what it takes to make data reuseable by others. Such bottom-up and community-driven approaches need to be valued by the research community, supported by publishers, and provided with long-term sustainable support by funding bodies and government. At the same time, these databases need to be linked to generic databases where possible, in order to be discoverable to the majority of researchers and thus promote effective and efficient data sharing. As we look forward to a future that embraces open access to data and publications, it is essential that data policies, data curation, data integration, data infrastructure, and data funding are linked together so as to foster data access and research productivity