Media

Reproducibility

Books

• The Turing Way
• Rigor Mortis: How Sloppy Science Creates Worthless Cures, Crushes Hope, and Wastes Billions
• Bad Science
• Bad pharma
• Science Fictions: How Fraud, Bias, Negligence, and Hype Undermine the Search for Truth
• Reproducibility and Replicability in Science
• Doctored: Fraud, Arrogance, and Tragedy in the Quest to Cure Alzheimer’s

For the purposes of giving good feedback when critiquing and being critiqued

• Thanks for the feedback the science and art of receiving feedback well (even when it is off base, unfair, poorly delivered, and frankly, you’re not in the mood)

Podcasts

• ReproducibiliTea
• ORION open science
• FAIR data podcast
• Code for Thought
• Access 2 Perspectives

Video

• The UK Reproducibility Network (UKRN) YouTube Channel

Websites & Blogs

• Data Colada
• Retraction Watch
• PubPeer
• Science Integrity Digest - Elizabeth Bik
• Experimental History - Adam Mastroianni

Papers other scholarly publications

• Reroducibility Project: Cancer Biology - collection of papers
• Garijo et al. (2013)
• Markowetz (2015)
• Trisovic et al. (2022)
• European Commission. Directorate General for Research and Innovation. and PwC EU Services. (2018)
• Hinsen (2018)
• Braga et al. (2023)

Organisations

• The UK Reproducibility Network (UKRN)
• Open Life Science (OLS)
• Center for Open Science
• Good Science Project

Graphics and Data Visualisation

Training & Workshops

• look out for the scientific figure design & ggplot courses from Babraham Bioinformatics

Books

• Building Science Graphics - I leave my copy of this one in the fishbowl if anyone wants to borrow it
• A Field Guide to Digital Color
• The Grammar of Graphics
• The Visual Display of Quantitative Information
• Data Visualization for Biomedical Scientists: Creating Tables and Graphs That Work by Maarten Boers see also the Accompanying free online course

Podcasts

• Data Viz Today
• Data Stories
• PolicyViz

Video

• Outline of grammar of grphics
  • A Grammar of Graphics - Excellent summary of the grammar of graphics layers or ‘functional pipeline’
  • Leland Wilkinson - The Grammar of Graphics - Leland himself giving a quick high level summary of the grammar of graphics
• Martin Krzywinski: A pandemic of bad charts
• EMBL Keynote Lecture 2019 - Data visualization and data science, Hadley Wickham
• Practical high level intros to Tufte’s principles
  • What should we do to improve our graphics and figures?
  • Graphical Excellence

Organisations

• biovis

Websites & Blogs

• A Comprehensive Guide to the Grammar of Graphics for Effective Visualization of Multi-dimensional Data - a shorter more accessible introduction to the grammar of graphics than Leland’s book or Hadley’s paper

Papers other scholarly publications

• A layered grammar of graphics (Wickham 2010)

References

Braga, Pedro Henrique Pereira, Katherine Hébert, Emma J. Hudgins, Eric R. Scott, Brandon P. M. Edwards, Luna L. Sánchez Reyes, Matthew J. Grainger, et al. 2023. “Not Just for Programmers: How GitHub Can Accelerate Collaborative and Reproducible Research in Ecology and Evolution.” Methods in Ecology and Evolution 14 (6): 1364–80. https://doi.org/10.1111/2041-210x.14108.

European Commission. Directorate General for Research and Innovation., and PwC EU Services. 2018. Cost-benefit analysis for FAIR research data: cost of not having FAIR research data. LU: Publications Office. https://doi.org/10.2777/02999.

Garijo, Daniel, Sarah Kinnings, Li Xie, Lei Xie, Yinliang Zhang, Philip E. Bourne, and Yolanda Gil. 2013. “Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome.” Edited by Christos A. Ouzounis. PLoS ONE 8 (11): e80278. https://doi.org/10.1371/journal.pone.0080278.

Hinsen, Konrad. 2018. “Verifiability in Computer-Aided Research: The Role of Digital Scientific Notations at the Human-Computer Interface.” PeerJ Computer Science 4 (July): e158. https://doi.org/10.7717/peerj-cs.158.

Markowetz, Florian. 2015. “Five Selfish Reasons to Work Reproducibly.” Genome Biology 16 (1). https://doi.org/10.1186/s13059-015-0850-7.

Trisovic, Ana, Matthew K. Lau, Thomas Pasquier, and Mercè Crosas. 2022. “A Large-Scale Study on Research Code Quality and Execution.” Scientific Data 9 (1). https://doi.org/10.1038/s41597-022-01143-6.

Wickham, Hadley. 2010. “A Layered Grammar of Graphics.” Journal of Computational and Graphical Statistics 19 (1): 3–28. https://doi.org/10.1198/jcgs.2009.07098.