We construct a graph of dependencies between software packages mentioned in the CZI Software Mentions Dataset. We then use the Katz centrality score to rank the importance of each software package. The data is available as Brown, E. M. (2023). A Dependency Graph for 460,000 Papers and Their Software Mentions from the CZI Software Mentions Dataset (1.0.0) [Data set]. CZI Research Software Hackathon. Zenodo. https://doi.org/10.5281/zenodo.10048132.
We find some interesting examples of "most important" (given that some of the ecosystems are incorrectly labelled):
- PACE is the most mentioned software but may not be the most "critical" / connected
- VELVET is seemingly the "most critical" / connected software that has very few mentions
- PERMANOVA is seemingly a "true" (mentioned and identified in the correct ecosystem) which is incredidly important and correct and has a number of mentions.
All of these are NEVER mentioned.
PyPI - six: Python 2 and 3 compatibility utilities.
Bioconductor - BiocIO: a package for basic file handling and some formats
CRAN - isoband: An R package to generate contour lines and polygons.
Exploring the Dependencies of Imported Software within Notebooks from the Combined CZI Software Mentions Dataset and
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