Computational reproducibility of Jupyter notebooks from biomedical publications

S Samuel, D Mietchen - GigaScience, 2024 - academic.oup.com
Background Jupyter notebooks facilitate the bundling of executable code with its
documentation and output in one interactive environment, and they represent a popular …

[PDF][PDF] Discovering data sets through machine learning: An ensemble approach to uncovering the prevalence of government-funded data sets

R Hausen, H Azarbonyad - Harvard Data Science Review, 2024 - assets.pubpub.org
The prevalence of government-funded dataset usage has yet to be comprehensively tracked
and understood. The lack of a standardized citation methodology has thus far prevented the …

[HTML][HTML] Retracted articles use less free and open-source software and cite it worse

D Schindler, E Yan, S Spors, F Krüger - Quantitative Science Studies, 2023 - direct.mit.edu
As an essential mechanism of scientific self-correction, articles are retracted for many
reasons, including errors in processing data and computation of results. In today's data …

Bidirectional paper-repository tracing in software engineering

D Garijo, M Arroyo, E Gonzalez… - 2024 IEEE/ACM 21st …, 2024 - ieeexplore.ieee.org
While computer science papers frequently include their associated code repositories,
establishing a clear link between papers and their corresponding implementations may be …

A multi-level analysis of data quality for formal software citation

D Schindler, T Hossain, S Spors… - Quantitative Science …, 2024 - direct.mit.edu
Software is a central part of modern science, and knowledge of its use is crucial for the
scientific community with respect to reproducibility and attribution of its developers. Several …

FAIRSECO: An Extensible Framework for Impact Measurement of Research Software

S Farshidi, J Maassen, R Bakhshi… - 2023 IEEE 19th …, 2023 - ieeexplore.ieee.org
The growing usage of research software in the research community has highlighted the
need to recognize and acknowledge the contributions made not only by researchers but …

[HTML][HTML] An RML-FNML module for Python user-defined functions in Morph-KGC

J Arenas-Guerrero, P Espinoza-Arias, JA Bernabé-Diaz… - SoftwareX, 2024 - Elsevier
The RML mapping language declares schema transformations to map heterogeneous data
into knowledge graphs. Although the schema transformations provided by RML are sufficient …

Perspectives on tracking data reuse across biodata resources

KE Ross, FB Bastian, M Buys, CE Cook… - Bioinformatics …, 2024 - academic.oup.com
Motivation Data reuse is a common and vital practice in molecular biology and enables the
knowledge gathered over recent decades to drive discovery and innovation in the life …

Empowering Knowledge Discovery from Scientific Literature: A novel approach to Research Artifact Analysis

P Stavropoulos, I Lyris, N Manola… - Proceedings of the …, 2023 - aclanthology.org
Abstract Knowledge extraction from scientific literature is a major issue, crucial to promoting
transparency, reproducibility, and innovation in the research community. In this work, we …

Don't mention it: An approach to assess challenges to using software mentions for citation and discoverability research

S Druskat, NPC Hong, S Buzzard, O Konovalov… - arXiv preprint arXiv …, 2024 - arxiv.org
Datasets collecting software mentions from scholarly publications can potentially be used for
research into the software that has been used in the published research, as well as into the …