Nine best practices for research software registries and repositories

Garijo, Daniel; Ménager, Hervé; Hwang, Lorraine; Trisovic, A.; Hucka, Michael; Morrell, Thomas E.; Allen, Alice

doi:10.7717/peerj-cs.1023

Cited by 7 publications

(7 citation statements)

References 52 publications

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“…Finally, they discussed implications for software citation advocacy and standard making efforts seeking to improve the situation. Garijo et al (2022) : “Nine best practices for research software registries and repositories.” Differing from the previous papers, this work was about the role of registries and repositories that aim to include software in their contents. These systems have a key role in supporting and improving software findability and research transparency, providing information for software citations, and fostering preservation of computational methods in a wide range of disciplines.…”

Section: Papers and Impactmentioning

confidence: 99%

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Special issue on software citation, indexing, and discoverability

Katz,

Chue Hong

2024

PeerJ Computer Science

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Software plays a fundamental role in research as a tool, an output, or even as an object of study. This special issue on software citation, indexing, and discoverability brings together five papers examining different aspects of how the use of software is recorded and made available to others. It describes new work on datasets that enable large-scale analysis of the evolution of software usage and citation, that presents evidence of increased citation rates when software artifacts are released, that provides guidance for registries and repositories to support software citation and findability, and that shows there are still barriers to improving and formalising software citation and publication practice. As the use of software increases further, driven by modern research methods, addressing the barriers to software citation and discoverability will encourage greater sharing and reuse of software, in turn enabling research progress.

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Section: Papers and Impactmentioning

confidence: 99%

“… Garijo et al (2022) discusses important practices for repositories and registries that store or refer to software. Having a set of such practices leads to more better citations, indexing, and discoverability of software as used in papers and other research works.…”

Section: Papers and Impactmentioning

confidence: 99%

Special issue on software citation, indexing, and discoverability

Katz,

Chue Hong

2024

PeerJ Computer Science

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“…[MR3] Allow for and make use of domain-specific metadata and make it possible to add new metadata schemes in a modular way using standardized format descriptions. Metadata schemes should be shared [25]. Use standardized formats such as DDI [W14], DataCite [50], EngMeta [51], and CodeMeta [52].…”

Section: Box 7: Recommendations For Multi-modal Data Repositoriesmentioning

confidence: 99%

“…In this work, we want to establish the basis for a sustainable research software lifecycle as shown in Fig. 1, combining best research software development practices [24,25] with sustainable and FAIR archival infrastructure [26][27][28]. We allow for a distributed view on data storage, where various research software artifacts may be stored in different (possibly specialized) data repositories, however, always cross-linked and FAIR.…”

Section: Introductionmentioning

confidence: 99%

A sustainable infrastructure concept for improved accessibility, reusability, and archival of research software

Koch¹,

Gläser²,

Seeland³

et al. 2023

Preprint

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Research software is an integral part of most research today and it is widely accepted that research software artifacts should be accessible and reproducible. However, the sustainable archival of research software artifacts is an ongoing effort. We identify research software artifacts as snapshots of the current state of research and an integral part of a sustainable cycle of software development, research, and publication. We develop requirements and recommendations to improve the archival, access, and reuse of research software artifacts based on installable, configurable, extensible research software, and sustainable public openaccess infrastructure. The described goal is to enable the reuse and exploration of research software beyond published research results, in parallel with reproducibility efforts, and in line with the FAIR principles for data and software. Research software artifacts can be reused in varying scenarios. To this end, we design a multi-modal representation concept supporting multiple reuse scenarios. We identify types of research software artifacts that can be viewed as different modes of the same software-based research result, for example, installation-free configurable browser-based apps to containerized environments, descriptions in journal publications and software documentation, or source code with installation instructions. We discuss how the sustainability and reuse of research software are enhanced or enabled by a suitable archive infrastructure. Finally, at the example of a pilot project at the University of Stuttgart, Germany-a collaborative effort between research software developers and infrastructure providers-we outline practical challenges and experiences.

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“…The three main categories of open RDRs are:Domain-specific or discipline repositories (DRs) which are used to store research data on the specific subject areas (Garijo et al. , 2022), for example, National Institutes of Health (NIH) data repositories for medical research data which are maintained by the Trans-NIH Biomedical Informatics Coordinating Committee (BMIC) (Gonzales et al.…”

Section: Introduction and Theoretical Backgroundmentioning

confidence: 99%

The utilisation of open research data repositories for storing and sharing research data in higher learning institutions in Tanzania

Mosha,

Ngulube

2023

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PurposeThe study aims to investigate the utilisation of open research data repositories (RDRs) for storing and sharing research data in higher learning institutions (HLIs) in Tanzania.Design/methodology/approachA survey research design was employed to collect data from postgraduate students at the Nelson Mandela African Institution of Science and Technology (NM-AIST) in Arusha, Tanzania. The data were collected and analysed quantitatively and qualitatively. A census sampling technique was employed to select the sample size for this study. The quantitative data were analysed using the Statistical Package for the Social Sciences (SPSS), whilst the qualitative data were analysed thematically.FindingsLess than half of the respondents were aware of and were using open RDRs, including Zenodo, DataVerse, Dryad, OMERO, GitHub and Mendeley data repositories. More than half of the respondents were not willing to share research data and cited a lack of ownership after storing their research data in most of the open RDRs and data security. HILs need to conduct training on using trusted repositories and motivate postgraduate students to utilise open repositories (ORs). The challenges for underutilisation of open RDRs were a lack of policies governing the storage and sharing of research data and grant constraints.Originality/valueResearch data storage and sharing are of great interest to researchers in HILs to inform them to implement open RDRs to support these researchers. Open RDRs increase visibility within HILs and reduce research data loss, and research works will be cited and used publicly. This paper identifies the potential for additional studies focussed on this area.

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Nine best practices for research software registries and repositories

Cited by 7 publications

References 52 publications

Special issue on software citation, indexing, and discoverability

Special issue on software citation, indexing, and discoverability

A sustainable infrastructure concept for improved accessibility, reusability, and archival of research software

The utilisation of open research data repositories for storing and sharing research data in higher learning institutions in Tanzania

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