{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/biomedical-open-source-software-crucial","title":"Biomedical Open Source Software: Crucial Packages and Hidden Heroes","arxiv_id":"2404.06672","date":"2024-04-10","proceeding":null,"authors":["Eva Maxfield Brown","Stephan Druskat","Laurent Hébert-Dufresne","James Howison","Daniel Mietchen","Andrew Nesbitt","João Felipe Pimentel","Boris Veytsman"],"abstract":"Despite the importance of scientific software for research, it is often not formally recognized and 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.","url_abs":"https://arxiv.org/abs/2404.06672v4","url_pdf":"https://arxiv.org/pdf/2404.06672v4.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"biomedical-open-source-software-crucial","repo_url":"https://github.com/borisveytsman/SoftwareImpactHackathon2023_Tracing_dependencies","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null},{"paper_slug":"biomedical-open-source-software-crucial","repo_url":"https://github.com/chanzuckerberg/software-impact-hackathon-2023","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[{"slug":"a-dependency-graph-for-460000-papers-and","name":"A Dependency Graph for 460,000 Papers and Their Software Mentions from the CZI Software Mentions Dataset","full_name":""}],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}