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 …
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 …
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
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 …
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 …
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 …
scientific community with respect to reproducibility and attribution of its developers. Several …
FAIRSECO: An Extensible Framework for Impact Measurement of Research Software
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 …
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 …
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 …
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 …
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
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 …
research into the software that has been used in the published research, as well as into the …