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  1. Article ; Online: Special issue on software citation, indexing, and discoverability.

    Katz, Daniel S / Chue Hong, Neil P

    PeerJ. Computer science

    2024  Volume 10, Page(s) e1951

    Abstract: 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 ... ...

    Abstract 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.
    Language English
    Publishing date 2024-03-26
    Publishing country United States
    Document type Editorial
    ISSN 2376-5992
    ISSN (online) 2376-5992
    DOI 10.7717/peerj-cs.1951
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online: Overcoming Challenges to Continuous Integration in HPC

    Gamblin, Todd / Katz, Daniel S.

    2023  

    Abstract: Continuous integration (CI) has become a ubiquitous practice in modern software development, with major code hosting services offering free automation on popular platforms. CI offers major benefits, as it enables detecting bugs in code prior to ... ...

    Abstract Continuous integration (CI) has become a ubiquitous practice in modern software development, with major code hosting services offering free automation on popular platforms. CI offers major benefits, as it enables detecting bugs in code prior to committing changes. While high-performance computing (HPC) research relies heavily on software, HPC machines are not considered "common" platforms. This presents several challenges that hinder the adoption of CI in HPC environments, making it difficult to maintain bug-free HPC projects, and resulting in adverse effects on the research community. In this article, we explore the challenges that impede HPC CI, such as hardware diversity, security, isolation, administrative policies, and non-standard authentication, environments, and job submission mechanisms. We propose several solutions that could enhance the quality of HPC software and the experience of developers. Implementing these solutions would require significant changes at HPC centers, but if these changes are made, it would ultimately enable faster and better science.
    Keywords Computer Science - Distributed ; Parallel ; and Cluster Computing
    Subject code 000
    Publishing date 2023-03-29
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Online: Research Software Engineering in 2030

    Katz, Daniel S. / Hettrick, Simon

    2023  

    Abstract: This position paper for an invited talk on the "Future of eScience" discusses the Research Software Engineering Movement and where it might be in 2030. Because of the authors' experiences, it is aimed globally but with examples that focus on the United ... ...

    Abstract This position paper for an invited talk on the "Future of eScience" discusses the Research Software Engineering Movement and where it might be in 2030. Because of the authors' experiences, it is aimed globally but with examples that focus on the United States and United Kingdom.

    Comment: Invited paper for 2023 IEEE Conference on eScience
    Keywords Computer Science - Software Engineering
    Publishing date 2023-08-15
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Group authorship, an excellent opportunity laced with ethical, legal and technical challenges.

    Hosseini, Mohammad / Holcombe, Alex O / Kovacs, Marton / Zwart, Hub / Katz, Daniel S / Holmes, Kristi

    Accountability in research

    2024  , Page(s) 1–23

    Abstract: Group authorship (also known as corporate authorship, team authorship, consortium authorship) refers to attribution practices that use the name of a collective (be it team, group, project, corporation, or consortium) in the authorship byline. Data shows ... ...

    Abstract Group authorship (also known as corporate authorship, team authorship, consortium authorship) refers to attribution practices that use the name of a collective (be it team, group, project, corporation, or consortium) in the authorship byline. Data shows that group authorships are on the rise but thus far, in scholarly discussions about authorship, they have not gained much specific attention. Group authorship can minimize tensions within the group about authorship order and the criteria used for inclusion/exclusion of individual authors. However, current use of group authorships has drawbacks, such as ethical challenges associated with the attribution of credit and responsibilities, legal challenges regarding how copyrights are handled, and technical challenges related to the lack of persistent identifiers (PIDs), such as ORCID, for groups. We offer two recommendations: 1) Journals should develop and share context-specific and unambiguous guidelines for group authorship, for which they can use the four baseline requirements offered in this paper; 2) Using persistent identifiers for groups and consistent reporting of members' contributions should be facilitated through devising PIDs for groups and linking these to the ORCIDs of their individual contributors and the Digital Object Identifier (DOI) of the published item.
    Language English
    Publishing date 2024-03-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2069334-5
    ISSN 1545-5815 ; 0898-9621
    ISSN (online) 1545-5815
    ISSN 0898-9621
    DOI 10.1080/08989621.2024.2322557
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: FAIR-USE4OS: Guidelines for creating impactful open-source software.

    Sonabend, Raphael / Gruson, Hugo / Wolansky, Leo / Kiragga, Agnes / Katz, Daniel S

    PLoS computational biology

    2024  Volume 20, Issue 5, Page(s) e1012045

    Abstract: This paper extends the FAIR (Findable, Accessible, Interoperable, Reusable) guidelines to provide criteria for assessing if software conforms to best practices in open source. By adding "USE" (User-Centered, Sustainable, Equitable), software development ... ...

    Abstract This paper extends the FAIR (Findable, Accessible, Interoperable, Reusable) guidelines to provide criteria for assessing if software conforms to best practices in open source. By adding "USE" (User-Centered, Sustainable, Equitable), software development can adhere to open source best practice by incorporating user-input early on, ensuring front-end designs are accessible to all possible stakeholders, and planning long-term sustainability alongside software design. The FAIR-USE4OS guidelines will allow funders and researchers to more effectively evaluate and plan open-source software projects. There is good evidence of funders increasingly mandating that all funded research software is open source; however, even under the FAIR guidelines, this could simply mean software released on public repositories with a Zenodo DOI. By creating FAIR-USE software, best practice can be demonstrated from the very beginning of the design process and the software has the greatest chance of success by being impactful.
    MeSH term(s) Software ; Guidelines as Topic ; Computational Biology/methods ; Software Design ; Humans
    Language English
    Publishing date 2024-05-09
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1012045
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Taking a fresh look at FAIR for research software.

    Katz, Daniel S / Gruenpeter, Morane / Honeyman, Tom

    Patterns (New York, N.Y.)

    2021  Volume 2, Issue 3, Page(s) 100222

    Abstract: Software is increasingly essential in most research, and much of this software is developed specifically for and during research. To make this research software findable, accessible, interoperable, and reusable (FAIR), we need to define exactly what FAIR ...

    Abstract Software is increasingly essential in most research, and much of this software is developed specifically for and during research. To make this research software findable, accessible, interoperable, and reusable (FAIR), we need to define exactly what FAIR means for research software and acknowledge that software is a living and complex object for which it is impossible to propose one solution that fits all software.
    Language English
    Publishing date 2021-03-12
    Publishing country United States
    Document type News
    ISSN 2666-3899
    ISSN (online) 2666-3899
    DOI 10.1016/j.patter.2021.100222
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Erratum: Taking a fresh look at FAIR for research software.

    Katz, Daniel S / Gruenpeter, Morane / Honeyman, Tom

    Patterns (New York, N.Y.)

    2021  Volume 2, Issue 5, Page(s) 100267

    Abstract: This corrects the article DOI: 10.1016/j.patter.2021.100222.]. ...

    Abstract [This corrects the article DOI: 10.1016/j.patter.2021.100222.].
    Language English
    Publishing date 2021-05-14
    Publishing country United States
    Document type Published Erratum
    ISSN 2666-3899
    ISSN (online) 2666-3899
    DOI 10.1016/j.patter.2021.100267
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: The effects of invertebrate herbivores on plant population growth: a meta-regression analysis.

    Katz, Daniel S W

    Oecologia

    2016  Volume 182, Issue 1, Page(s) 43–53

    Abstract: Over the last two decades, an increasing number of studies have quantified the effects of herbivory on plant populations using stage-structured population models and integral projection models, allowing for the calculation of plant population growth ... ...

    Abstract Over the last two decades, an increasing number of studies have quantified the effects of herbivory on plant populations using stage-structured population models and integral projection models, allowing for the calculation of plant population growth rates (λ) with and without herbivory. In this paper, I assembled 29 studies and conducted a meta-regression to determine the importance of invertebrate herbivores to population growth rates (λ) while accounting for missing data. I found that invertebrate herbivory often induced important reductions in plant population growth rates (with herbivory, λ was 1.08 ± 0.36; without herbivory, λ was 1.28 ± 0.58). This relationship tended to be weaker for seed predation than for other types of herbivory, except when seed predation rates were very high. Even so, the amount by which studies reduced herbivory was a poor predictor of differences in population growth rates-which strongly cautions against using measured herbivory rates as a proxy for the impact of herbivores. Herbivory reduced plant population growth rates significantly more when potential growth rates were high, which helps to explain why there was less variation in actual population growth rates than in potential population growth rates. The synthesis of these studies also shows the need for future studies to report variance in estimates of λ and to quantify how λ varies as a function of plant density.
    MeSH term(s) Animals ; Herbivory ; Insecta/drug effects ; Invertebrates ; Population Growth ; Regression Analysis
    Language English
    Publishing date 2016-09
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 123369-5
    ISSN 1432-1939 ; 0029-8549
    ISSN (online) 1432-1939
    ISSN 0029-8549
    DOI 10.1007/s00442-016-3602-9
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    In stock of ZB MED Bonn / Germany

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  9. Book ; Online: Research Software Engineers

    Cosden, Ian A. / McHenry, Kenton / Katz, Daniel S.

    Career Entry Points and Training Gaps

    2022  

    Abstract: As software has become more essential to research across disciplines, and as the recognition of this fact has grown, the importance of professionalizing the development and maintenance of this software has also increased. The community of software ... ...

    Abstract As software has become more essential to research across disciplines, and as the recognition of this fact has grown, the importance of professionalizing the development and maintenance of this software has also increased. The community of software professionals who work on this software have come together under the title Research Software Engineer (RSE) over the last decade. This has led to the formalization of RSE roles and organized RSE groups in universities, national labs, and industry. This, in turn, has created the need to understand how RSEs come into this profession and into these groups, how to further promote this career path to potential members, as well as the need to understand what training gaps need to be filled for RSEs coming from different entry points. We have categorized three main classifications of entry paths into the RSE profession and identified key elements, both advantages and disadvantages, that should be acknowledged and addressed by the broader research community in order to attract and retain a talented and diverse pool of future RSEs.

    Comment: Accepted by IEEE Computing in Science & Engineering (CiSE): Special Issue on the Future of Research Software Engineers in the US
    Keywords Computer Science - Software Engineering
    Subject code 303
    Publishing date 2022-10-09
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Urban-scale variation in pollen concentrations: A single station is insufficient to characterize daily exposure.

    Katz, Daniel S W / Batterman, Stuart A

    Aerobiologia

    2020  Volume 36, Issue 3, Page(s) 417–431

    Abstract: Epidemiological analyses of airborne allergenic pollen often use concentration measurements from a single station to represent exposure across a city, but this approach does not account for the spatial variation of concentrations within the city. Because ...

    Abstract Epidemiological analyses of airborne allergenic pollen often use concentration measurements from a single station to represent exposure across a city, but this approach does not account for the spatial variation of concentrations within the city. Because there are few descriptions of urban-scale variation, the resulting exposure measurement error is unknown but potentially important for epidemiological studies. This study examines urban scale variation in pollen concentrations by measuring pollen concentrations of 13 taxa over 24-hr periods twice weekly at 25 sites in two seasons in Detroit, Michigan. Spatio-temporal variation is described using cumulative distribution functions and regression models. Daily pollen concentrations across the 25 stations varied considerably, and the average quartile coefficient of dispersion was 0.63. Measurements at a single site explained 3-85% of the variation at other sites, depending on the taxon, and 95% prediction intervals of pollen concentrations generally spanned one to two orders of magnitude. These results demonstrate considerable heterogeneity of pollen levels at the urban scale, and suggest that the use of a single monitoring site will not reflect pollen exposure over an urban area and can lead to sizable measurement error in epidemiological studies, particularly when a daily time-step is used. These errors might be reduced by using predictive daily pollen levels in models that combine vegetation maps, pollen production estimates, phenology models and dispersion processes, or by using coarser time-steps in the epidemiological analysis.
    Language English
    Publishing date 2020-04-20
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1499126-3
    ISSN 1573-3025 ; 0393-5965
    ISSN (online) 1573-3025
    ISSN 0393-5965
    DOI 10.1007/s10453-020-09641-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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