James Howison
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View article: Report of the 2025 Workshop on Next-Generation Ecosystems for Scientific Computing: Harnessing Community, Software, and AI for Cross-Disciplinary Team Science
Report of the 2025 Workshop on Next-Generation Ecosystems for Scientific Computing: Harnessing Community, Software, and AI for Cross-Disciplinary Team Science Open
This report summarizes insights from the 2025 Workshop on Next-Generation Ecosystems for Scientific Computing: Harnessing Community, Software, and AI for Cross-Disciplinary Team Science, which convened more than 40 experts from national la…
View article: Use as Directed? A Comparison of Software Tools Intended to Check Rigor and Transparency of Published Work
Use as Directed? A Comparison of Software Tools Intended to Check Rigor and Transparency of Published Work Open
The causes of the reproducibility crisis include lack of standardization and transparency in scientific reporting. Checklists such as ARRIVE and CONSORT seek to improve transparency, but they are not always followed by authors and peer rev…
View article: Open source software field research: Spanning social and practice networks for re-entering the field
Open source software field research: Spanning social and practice networks for re-entering the field Open
Sociotechnical research increasingly includes the social sub-networks that emerge from large-scale sociotechnical infrastructure, including the infrastructure for building open source software. This paper addresses these numerous sub-netwo…
View article: Tales of Transitions: Seeking Scientific Software Sustainability
Tales of Transitions: Seeking Scientific Software Sustainability Open
Software is crucial to science, but sustaining projects for long term impact is challenging. Scientists and funders look to ''the open source way'' (known as peer production in the organizational literature) as a promising route to sustain…
View article: Paradoxes of Openness: Trans Experiences in Open Source Software
Paradoxes of Openness: Trans Experiences in Open Source Software Open
In recent years, concerns have increased over the lack of contributor diversity in open source software (OSS), despite its status as a paragon of open collaboration. OSS is an important form of digital infrastructure and part of a career p…
View article: Biomedical Open Source Software: Crucial Packages and Hidden Heroes
Biomedical Open Source Software: Crucial Packages and Hidden Heroes Open
Despite the importance of scientific software for research, it is often not formally recognized and rewarded. This is especially true for foundational libraries, which are hidden below packages visible to the users (and thus doubly hidden,…
View article: Codes of Conduct in Open Source
Codes of Conduct in Open Source Open
Hana Frluckaj, James Howison, Qiwei Li, and Laura Dabbish
View article: Softcite Dataset Version 2
Softcite Dataset Version 2 Open
This is the version 2.0 of the Softcite Dataset, a corpus of currently 4971 scientific articles with software mention annotations. This is a gold standard corpus, resulting from multi-stage annotations by a team of annotators and reconcili…
View article: Softcite Dataset Version 2
Softcite Dataset Version 2 Open
This is the version 2.0 of the Softcite Dataset, a corpus of currently 4971 scientific articles with software mention annotations. This is a gold standard corpus, resulting from multi-stage annotations by a team of annotators and reconcili…
View article: Understanding progress in software citation: a study of software citation in the CORD-19 corpus
Understanding progress in software citation: a study of software citation in the CORD-19 corpus Open
In this paper, we investigate progress toward improved software citation by examining current software citation practices. We first introduce our machine learning based data pipeline that extracts software mentions from the CORD-19 corpus,…
View article: Mining Software Entities in Scientific Literature
Mining Software Entities in Scientific Literature Open
We present a comprehensive information extraction system dedicated to software entities in scientific literature. This task combines the complexity of automatic reading of scientific documents (PDF processing, document structuring, styled/…
View article: Softcite software mention extraction from the CORD-19 publications
Softcite software mention extraction from the CORD-19 publications Open
Softcite software mention extraction from the CORD-19 publications This dataset is the result of the extraction of software mentions from the set of publications of the CORD-19 corpus (https://allenai.org/data/cord-19) by the Softcite sof…
View article: Softcite software mention extraction from the CORD-19 publications
Softcite software mention extraction from the CORD-19 publications Open
Softcite software mention extraction from the CORD-19 publications This dataset is the result of the extraction of software mentions from the set of publications of the CORD-19 corpus (https://allenai.org/data/cord-19) by the Softcite sof…
View article: Softcite software mention extraction from the CORD-19 publications
Softcite software mention extraction from the CORD-19 publications Open
Softcite software mention extraction from the CORD-19 publications This dataset is the first result of the extraction of software mentions from the set of publications of the CORD-19 corpus (https://allenai.org/data/cord-19) by the Softci…
View article: Softcite software mention extraction from the CORD-19 publications
Softcite software mention extraction from the CORD-19 publications Open
Softcite software mention extraction from the CORD-19 publications This dataset is the first result of the extraction of software mentions from the set of publications of the CORD-19 corpus (https://allenai.org/data/cord-19) by the Softci…
View article: Softcite software mention extraction from the CORD-19 publications
Softcite software mention extraction from the CORD-19 publications Open
Softcite software mention extraction from the CORD-19 publications This dataset is the first result of the extraction of software mentions from the set of publications of the CORD-19 corpus (https://allenai.org/data/cord-19) by the Softci…
View article: Softcite Dataset: A dataset of software mentions in research publications
Softcite Dataset: A dataset of software mentions in research publications Open
The Softcite dataset is a gold-standard dataset of software mentions in research publications, a free resource primarily for software entity recognition in scholarly text. This is the first release of this dataset. What's in the dataset Wi…
View article: Softcite Dataset: A dataset of software mentions in research publications
Softcite Dataset: A dataset of software mentions in research publications Open
The Softcite dataset is a gold-standard dataset of software mentions in research publications, a free resource primarily for software entity recognition in scholarly text. This is the first release of this dataset. What's in the dataset Wi…
View article: Guiding Development Work Across a Software Ecosystem by Visualizing Usage Data
Guiding Development Work Across a Software Ecosystem by Visualizing Usage Data Open
Software is increasingly produced in the form of ecosystems, collections of interdependent components maintained by a distributed community. These ecosystems act as network organizations, not markets, and thus often lack actionable price-l…
View article: The challenges of theory-software translation
The challenges of theory-software translation Open
Background: Software is now ubiquitous within research. In addition to the general challenges common to all software development projects, research software must also represent, manipulate, and provide data for complex theoretical construc…
View article: Large-scale refactoring challenges and coordination in open source software development
Large-scale refactoring challenges and coordination in open source software development Open
Increasingly complicated software makes it difficult to attract or maintain open source software (OSS) contributors. Faced with such challenges of increasingly complicated software design, large-scale refactoring that radically restructure…
View article: Large-scale refactoring challenges and coordination in open source software development
Large-scale refactoring challenges and coordination in open source software development Open
Increasingly complicated software makes it difficult to attract or maintain open source software (OSS) contributors. Faced with such challenges of increasingly complicated software design, large-scale refactoring that radically restructure…
View article: Theory-Software Translation: Research Challenges and Future Directions
Theory-Software Translation: Research Challenges and Future Directions Open
The Theory-Software Translation Workshop, held in New Orleans in February 2019, explored in depth the process of both instantiating theory in software - for example, implementing a mathematical model in code as part of a simulation - and u…
View article: Organizing and the Cyberinfrastructure Workforce
Organizing and the Cyberinfrastructure Workforce Open
A report from the NSF-sponsored “Cyberinfrastructure Workforce” workshop in Alexandria, Virginia, on August 14&15, 2017. The workshop is one of six workshops that comprise the Research Coordination Network (RCN) on Management of Collaborat…
View article: Collaboration through superposition: How the IT artifact as an object of collaboration affords technical interdependence without organizational interdependence
Collaboration through superposition: How the IT artifact as an object of collaboration affords technical interdependence without organizational interdependence Open
This paper develops a theory of collaboration through superposition: the process of depositing separate layers on top of each other over time. The theory is developed in a study of development of community-based Free and Open Source Softwa…
View article: Software makes science better, but is it research? DotAstonomy X Presentation
Software makes science better, but is it research? DotAstonomy X Presentation Open
Invited Presentation at .Astronomy X conference
View article: Lightning Talk: "I solemnly pledge": A Manifesto for Personal Responsibility in the Engineering of Academic Software
Lightning Talk: "I solemnly pledge": A Manifesto for Personal Responsibility in the Engineering of Academic Software Open
Software is fundamental to academic research work, both as part of the method and as the result of research. In June 2016 25 people gathered at Schloss Dagstuhl for a week-long Perspectives Workshop and began to develop a manifesto which p…
View article: Engineering Academic Software (Dagstuhl Perspectives Workshop 16252)
Engineering Academic Software (Dagstuhl Perspectives Workshop 16252) Open
Software is often a critical component of scientific research. It can be a component of the academic research methods used to produce research results, or it may itself be an academic research result. Software, however, has rarely been con…