Steps to Reproduce

1. Install dependencies using pip install -e . or with Just with just install.
2. Download some additional data files from: https://zenodo.org/records/10045415
   1. bioconductorwithmention_counts.ndjson.tar.gz
   2. cranwithmention_counts.ndjson.tar.gz
   3. pypiwithmentions.ndjson.tar.gz
   4. commdisambiguatedcvis_count.json.tar.gz
3. Decompress each of these files and place them in the data/ directory.
4. Run the preprocess.ipynb notebook in the notebooks/ directory. This will create the "dois-graph/full-graph.gexf" file in the data/ directory.
5. Run the directed-core-analysis.ipynb notebook in the notebooks/ directory. This will use the "dois-graph/full-graph.gexf" file in the data/ directory to create the "pruned-network.csv" and "pruned-network.gexf" files in the data/ directory.
6. Run the visualization.ipynb notebook in the notebooks/ directory. This will use the "pruned-network.csv" file in the data/ to create the final mentions over katz centrality visualization.

All other visualizations in the original paper are created directly in Gephi from the "pruned-network.gexf" file. In Gephi, node size represents Katz centrality with a factor of 4 between the minimum and maximum value, nodes then follow the Yifan Hu layout with optimal distance 100.0 and relative strength 0.2 on edges

Exploring the dependencies of the CZI mentions dataset

Exploring the Dependencies of Mentioned Software in the CZI Software Mentions Dataset

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.

Software That is Important but has No Mentions in the Literature

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

About this project

This repository was developed as part of the Mapping the Impact of Research Software in Science hackathon hosted by the Chan Zuckerberg Initiative (CZI). By participating in this hackathon, owners of this repository acknowledge the following: 1. The code for this project is hosted by the project contributors in a repository created from a template generated by CZI. The purpose of this template is to help ensure that repositories adhere to the hackathons project naming conventions and licensing recommendations. CZI does not claim any ownership or intellectual property on the outputs of the hackathon. This repository allows the contributing teams to maintain ownership of code after the project, and indicates that the code produced is not a CZI product, and CZI does not assume responsibility for assuring the legality, usability, safety, or security of the code produced. 2. This project is published under a MIT license.

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