Meeting the United Nation’ Sustainable Development Goals (SDGs) calls for an integrative scientific approach, combining expertise, data, models and tools across many disciplines towards addressing sustainability challenges at various spatial and temporal scales. This holistic approach, while necessary, exacerbates the big data and computational challenges already faced by researchers. Many challenges in sustainability research can be tackled by harnessing the power of advanced cyberinfrastructure (CI). The objective of this paper is to highlight the key components and technologies of CI necessary for meeting the data and computational needs of the SDG research community. An overview of the CI ecosystem in the United States is provided with a specific focus on the investments made by academic institutions, government agencies and industry at national, regional, and local levels. Despite these investments, this paper identifies barriers to the adoption of CI in sustainability research that include, but are not limited to access to support structures; recruitment, retention and nurturing of an agile workforce; and lack of local infrastructure. Relevant CI components such as data, software, computational resources, and human-centered advances are discussed to explore how to resolve the barriers. The paper highlights multiple challenges in pursuing SDGs based on the outcomes of several expert meetings. These include multi-scale integration of data and domain-specific models, availability and usability of data, uncertainty quantification, mismatch between spatiotemporal scales at which decisions are made and the information generated from scientific analysis, and scientific reproducibility. We discuss ongoing and future research for bridging CI and SDGs to address these challenges.
How Reproducibility Will Accelerate Discovery Through Collaboration in Physio-Logging
What new questions could ecophysiologists answer if physio-logging research was fully reproducible? We argue that technical debt (computational hurdles resulting from prioritizing short-term goals over long-term sustainability) stemming from insufficient cyberinfrastructure (field-wide tools, standards, and norms for analyzing and sharing data) trapped physio-logging in a scientific silo. This debt stifles comparative biological analyses and impedes interdisciplinary research. Although physio-loggers (e.g., heart rate monitors and accelerometers) opened new avenues of research, the explosion of complex datasets exceeded ecophysiology’s informatics capacity. Like many other scientific fields facing a deluge of complex data, ecophysiologists now struggle to share their data and tools. Adapting to this new era requires a change in mindset, from “data as a noun” (e.g., traits, counts) to “data as a sentence”, where measurements (nouns) are associate with transformations (verbs), parameters (adverbs), and metadata (adjectives). Computational reproducibility provides a framework for capturing the entire sentence. Though usually framed in terms of scientific integrity, reproducibility offers immediate benefits by promoting collaboration between individuals, groups, and entire fields. Rather than a tax on our productivity that benefits some nebulous greater good, reproducibility can accelerate the pace of discovery by removing obstacles and inviting a greater diversity of perspectives to advance science and society. In this article, we 1) describe the computational challenges facing physio-logging scientists and connect them to the concepts of technical debt and cyberinfrastructure , 2) demonstrate how other scientific fields overcame similar challenges by embracing computational reproducibility, and 3) present a framework to promote computational reproducibility in physio-logging, and bio-logging more generally.
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- Award ID(s):
- 2052497
- PAR ID:
- 10344264
- Date Published:
- Journal Name:
- Frontiers in Physiology
- Volume:
- 13
- ISSN:
- 1664-042X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract -
The scientific computing community has long taken a leadership role in understanding and assessing the relationship of reproducibility to cyberinfrastructure, ensuring that computational results - such as those from simulations - are "reproducible", that is, the same results are obtained when one re-uses the same input data, methods, software and analysis conditions. Starting almost a decade ago, the community has regularly published and advocated for advances in this area. In this article we trace this thinking and relate it to current national efforts, including the 2019 National Academies of Science, Engineering, and Medicine report on "Reproducibility and Replication in Science". To this end, this work considers high performance computing workflows that emphasize workflows combining traditional simulations (e.g. Molecular Dynamics simulations) with in situ analytics. We leverage an analysis of such workflows to (a) contextualize the 2019 National Academies of Science, Engineering, and Medicine report's recommendations in the HPC setting and (b) envision a path forward in the tradition of community driven approaches to reproducibility and the acceleration of science and discovery. The work also articulates avenues for future research at the intersection of transparency, reproducibility, and computational infrastructure that supports scientific discovery.more » « less
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Abstract In biomedical research, validating a scientific discovery hinges on the reproducibility of its experimental results. However, in genomics, the definition and implementation of reproducibility remain imprecise. We argue that genomic reproducibility, defined as the ability of bioinformatics tools to maintain consistent results across technical replicates, is essential for advancing scientific knowledge and medical applications. Initially, we examine different interpretations of reproducibility in genomics to clarify terms. Subsequently, we discuss the impact of bioinformatics tools on genomic reproducibility and explore methods for evaluating these tools regarding their effectiveness in ensuring genomic reproducibility. Finally, we recommend best practices to improve genomic reproducibility.
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Data sharing is an integral component of research and academic publications, allowing for independent verification of results. Researchers have the ability to extend and build upon prior research when they are able to efficiently access, validate, and verify the data referenced in publications. Despite the well known benefits of making research data more open, data withholding rates have remained constant. Some disincentives to sharing research data include lack of credit, and fear of misrepresentation of data in the absence of context and provenance. While there are several research data sharing repositories that focus on making research data available, there are no cyberinfrastructure platforms that enable researchers to efficiently validate the authenticity of datasets, track the provenance, view the lineage of the data and verify ownership information. In this paper, we introduce and provide an overview of the NSF funded Open Science Chain, a cyberinfrastructure platform built using blockchain technologies that securely stores metadata and verification information about research data and tracks changes to that data in an auditable manner in order to address issues related to reproducibility and accountability in scientific research.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3389/fphys.2022.917976
