ArticlePLoS computational biology2026
Biomedical open source software: Crucial packages and hidden heroes.
Article in PLoS computational biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite the importance of scientific software for research, it is often not formally recognized nor rewarded. This is especially true for foundational libraries, which are hidden below packages visible to the users (and thus doubly hidden, since even the packages directly used in research are frequently not visible in the paper). Research stakeholders like funders, infrastructure providers, and other organizations need to understand the complex network of computer programs that contemporary research relies upon. In this work, we use the CZ Software Mentions Dataset to map the upstream dependencies of software used in biomedical papers and find the packages critical to scientific software ecosystems. We propose centrality metrics for the network of software dependencies, analyze three ecosystems (PyPI, CRAN, Bioconductor), and determine the packages with the highest centrality.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.