GitHub statistics as a measure of the impact of open-source bioinformatics software

Scripts to reproduce all results in the "GitHub statistics as a measure of the impact of open-source bioinformatics software" paper, accepted in Frontiers in Bioengineering and Biotechnology, section Bioinformatics and Computational Biology, doi: 10.3389/fbioe.2018.00198.

Links

• star-history - The missing star history graph of GitHub repos - https://star-history.com

• Rxivist, bioinformatics authors - most cited authors in bioinformatics

• projmgr aims to better integrate project management into your workflow and free up time for more exciting tasks like R coding and data analysis. Since many R users and programmers use GitHub as a home for their analysis, the goal of projmgr is to streamline project management with these same tools.

• jdtrat/ghee - Provides a lightweight interface for Github through R

• metrumresearchgroup/ghpm is a library written in R that grabs and parses data from a github repository making it easier for users to perform analytics. Using Github's flexible GraphQL API and R's dataframe structure, ghpm returns repository data about issues, milestones, project boards, and pull requests which can be melded together to identify useful analytical information.

• GitDiscoverer - An app to discover trending repositories, trending developers and popular projects in ML/DL on Github. RStudio announcement

• GitMemory - history of github activity of individual users and repositories Github User Rank List

• The missing star history graph of github repos https://star-history.t9t.io, https://github.com/timqian/star-history

• fCite - fractional citation tool, better metric to quantify scientific output, an aggregate of several metrics (FLAE, FLAE2, FLAE3, EC). http://www.fcite.org/

  • Kozlowski, Lukasz Pawel. “FCite: A Fractional Citation Tool to Quantify an Individual’s Scientific Research Output.” Preprint. Scientific Communication and Education, September 21, 2019. https://doi.org/10.1101/771485.

• Gardner, Paul P., James M. Paterson, Stephanie McGimpsey, Fatemeh Ashari-Ghomi, Sinan U. Umu, Aleksandra Pawlik, Alex Gavryushkin, and Michael A. Black. “Sustained Software Development, Not Number of Citations or Journal Choice, Is Indicative of Accurate Bioinformatic Software.” Preprint. Bioinformatics, December 7, 2016. https://doi.org/10.1101/092205. https://github.com/Gardner-BinfLab/speed-vs-accuracy-meta-analysis, https://figshare.com/articles/dataset/Sustained_software_development_not_number_of_citations_or_journal_choice_is_indicative_of_accurate_bioinformatic_software_--_PubMed_XML_files/15121818/2

• A list of R developers and advocates on Github. https://github.com/amrrs/awesome_R_Githubers

• Meta-Research: Tracking the popularity and outcomes of all bioRxiv preprints, https://elifesciences.org/articles/45133

• Top 1% of highly cited researchers in 2018, https://hcr.clarivate.com/#

• Journal impact factor correlates with the number of their followers on Twitter, https://twitter.com/generegulation/status/1101537375962976262?s=03

• Tracking the popularity and outcomes of all bioRxiv preprints. https://www.bioverlay.org/post/2019-03-tracking-the-popularity-and-outcomes-of-all-biorxiv-preprints/, https://rxivist.org/

• Resumes generated using the GitHub informations. Web site, http://resume.github.io/, and GitHub source code, https://github.com/resume/resume.github.com

• "Top Biomedical GitHub Repos" - top 15 bioinformatics repositories (including Keras) with top citations. https://blog.semanticscholar.org/top-biomedical-github-repos-3ea15cf1930a

• Twitter accounts recommended to scientists working on gene regulation. https://generegulation.org/twitter-accounts-for-gene-regulation-scientists/

• How to use Twitter to further your research career, https://www.nature.com/articles/d41586-019-00535-w

• Bioinformatics-Workflow-Managers-Tools-Platforms-Languages-Specifications-Standards - who is who in #Bioinformatics #Workflow managers with repo metrics.

• API providing access to papers and authors scraped from biorxiv.org. Online, https://rxivist.org/, GitHub, https://github.com/blekhmanlab/rxivist

• "Reviewer-coerced citation: Case report, update on journal policy, and suggestions for future prevention" Jonathan D Wren, Alfonso Valencia, Janet Kelso. Bioinformatics, https://doi.org/10.1093/bioinformatics/btz071. Published: 30 January 2019.

• An updated ranking of institutes and countries based on developed biological databases is available at http://bigd.big.ac.cn/databasecommons/stat.

• A list of predatory journals, https://predatoryjournals.com/, GitHub, https://github.com/stop-predatory-journals/stop-predatory-journals.github.io

• statcheck - An R package and a web tool to extract statistics from articles and recompute p-values. http://statcheck.io/, https://cran.r-project.org/web/packages/statcheck/index.html, https://mbnuijten.com/statcheck/

• Introducing eLife’s first computationally reproducible article. https://elifesciences.org/labs/ad58f08d/introducing-elife-s-first-computationally-reproducible-article

Files

• Manuscript, PDF, Rmd

• Figure 1 - PCA of bioinformatics impact measures, colored by metric type. png

• Supplementary Figure 1 - Growth of publications in PubMed having the term "bioinformatics" in their title/abstract. Y-axis is the proportion of bioinformatics publications out of the total number of publications, in percent. png

• Supplementary Figure 2 - Correlogram of bioinformatics software impact metrics. Each cell shows Pearson Correlation Coefficient (PCC) for the corresponding pair of metrics. Blue/Red gradient highlights low/high PCC, respectively. png

• Table 1. Popular collections of bioinformatics resources. Accessed on 2018-11-30. Markdown

• Supplementary Tables, PDF

  • Supplementary Table 1. Select data science resources. Metrics in all tables were assessed on 2018-11-30. Markdown
  • Supplementary Table 2. Examples of lists of lists of computer science and machine learning resources. Markdown
  • Supplementary Table 3. Impact metrics of popular bioinformatics tools and resources. Only software that is being developed on GitHub, has over 50 stars, and published in peer-review journals was selected. Markdown

• More links to data science, bioinformatics, statistics, and machine learning resources, https://github.com/mdozmorov/blogs

• Open an issue to report additional resources. See closed issues for additional resources.

Compiling

• Download CiteScore_Metrics_2011-2017_Download_25May2018.xlsx, CiteScore metrics, into data folder. Downloaded from https://www.scopus.com/sources?dgcid=RN_AG_Sourced_300000264 on 10/22/2018. Requires login, click "Download Scopus Source List", then "Download source titles and metrics".
• Run scripts/citescore.R that will use data/CiteScore_Metrics_2011-2017_Download_25May2018.xlsx to create tables/CiteScore_2017.csv
• Run scripts/altmetrics.R that will use tables_altmetrics.csv to create Table_software_stats.csv
• Run figures_impact.Rmd that will use Table_software_stats.csv to create figures/Figure_bioinformatics_paper_growth.png, figures/Figure_impact_PCA.png, figures/Figure_correlations.png
• tables_impact.Rmd will create its own tables and use Table_software_stats.csv to create Supplementary Table 3

root

• manuscript_impact.Rmd, tables_impact.Rmd, figures_impact.Rmd - source files for the manuscript, tables, and figures, respectively

scripts

• altmetrics.R - extracting data from tables_altmetrics.csv
• citescore.R - extracting data from CiteScore_Metrics_2011-2017_Download_25May2018.xlsx
• utils.R - functions to make tables using GitHub API

styles

• Frontiers_Template.docx, frontiers-in-bioengineering-and-biotechnology.csl - Frontiers Word doc template and citation style, respectively.

tables

• CiteScore_2017.csv - CiteScore 2017 extracted with scripts/citescore.R
• tables_altmetrics.csv - GitHub repositories selected for the analysis. tables_altmetrics1.csv, tables_altmetrics2.csv - first and second parts of the extended list of GitHub repositories. Split in parts because unregistered GitHub API allows 60 queries/hour limit.
• Table_software_stats.csv - The final impact statistics table. Table_software_stats1.csv, Table_software_stats2.csv - first and second parts of the extended impact statistics table