Verifiability in computer-aided research: the role of digital scientific notations at the human-computer interface

Hinsen, Konrad

doi:10.7717/peerj-cs.158

Cited by 10 publications

(8 citation statements)

References 36 publications

(14 reference statements)

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“…Moreover, research papers discuss scientific results based on research software; but the research software behind the results is quickly outdated and developed further. Above all, the precise implementation of physic into code in the research software is not specified 31 , but particularly this point is essential for reusing the research software. Besides, articles document research results, not software.…”

Section: Discussionmentioning

confidence: 99%

Documenting Research Software in Engineering Science

Hermann

Fehr

2022

Preprint

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The reuse of research software needs good documentation, however, the documentation in particular is often criticized. Especially in non-IT specific disciplines, the lack of documentation is attributed to the lack of training, the lack of time or missing rewards. This article addresses the hypothesis that scientists do document but do not know exactly what they need to document, why, and for whom. In order to evaluate the actual documentation practice of research software, we examined existing recommendations, and we evaluated their implementation in everyday practice using a concrete example from the engineering sciences and compared the findings with best practice examples. In order to get a broad overview of what documentation of research software entailed, we defined categories and used them to conduct the research. Our results show that the big picture of what documentation of research software means is missing. Recommendations do not consider the important role of developers whose documentation takes mainly place in their research articles. Moreover, we show that research software always has a history that influences the documentation.

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Section: Discussionmentioning

confidence: 99%

Documenting Research Software in Engineering Science

Hermann

Fehr

2022

Preprint

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“…Moreover, research papers discuss scientific results based on research software; but the research software behind the results is quickly outdated and developed further. Above all, the precise implementation of physic into code in the research software is not specified 34 , but particularly this point is essential for reusing the research software. Besides, articles document research results, not software.…”

Section: Discussionmentioning

confidence: 99%

Documenting research software in engineering science

Schmitz

Fehr

2022

Sci Rep

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The reuse of research software needs good documentation, however, the documentation in particular is often criticized. Especially in non-IT specific disciplines, the lack of documentation is attributed to the lack of training, the lack of time or missing rewards. This article addresses the hypothesis that scientists do document but do not know exactly what they need to document, why, and for whom. In order to evaluate the actual documentation practice of research software, we examined existing recommendations, and we evaluated their implementation in everyday practice using a concrete example from the engineering sciences and compared the findings with best practice examples. To get a broad overview of what documentation of research software entailed, we defined categories and used them to conduct the research. Our results show that the big picture of what documentation of research software means is missing. Recommendations do not consider the important role of researchers, who write research software, whose documentation takes mainly place in their research articles. Moreover, we show that research software always has a history that influences the documentation.

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“…Thus, when wiring together containers in a scientific workflow, proper care needs to be taken that the observed output matches what would be expected from using the tool directly. 48 Also for this reason we strongly suggest to follow community best practices for packaging and containerization of bioinformatics software. 49…”

Section: Discussionmentioning

confidence: 99%

Approaches for containerized scientific workflows in cloud environments with applications in life science

et al. 2021

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Containers are gaining popularity in life science research as they provide a solution for encompassing dependencies of provisioned tools, simplify software installations for end users and offer a form of isolation between processes. Scientific workflows are ideal for chaining containers into data analysis pipelines to aid in creating reproducible analyses. In this article, we review a number of approaches to using containers as implemented in the workflow tools Nextflow, Galaxy, Pachyderm, Argo, Kubeflow, Luigi and SciPipe, when deployed in cloud environments. A particular focus is placed on the workflow tool’s interaction with the Kubernetes container orchestration framework.

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Verifiability in computer-aided research: the role of digital scientific notations at the human-computer interface

Cited by 10 publications

References 36 publications

Documenting Research Software in Engineering Science

Documenting Research Software in Engineering Science

Documenting research software in engineering science

Approaches for containerized scientific workflows in cloud environments with applications in life science

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