Data Science, GitHub, reproducibility, Tools & Resources

Lab manuals for data management and reproducibility

I am a collaborator in my institution’s Responsible Conduct in Research instruction. After one recent session on data management best practices, a postdoc participant requested a consultation with us. He wanted guidance about how to establish and maintain a lab culture that fosters reproducible science.

This question has taken on special urgency in the wake of the highly publicized case of former Stanford University President Dr. Marc Tessier-Lavigne. Last year articles were published in the Stanford student newspaper about anomalies in several of Tessier-Lavigne’s neuroscience articles that had been flagged on PubPeer. Ultimately an investigative committee report, issued in July 2023, found that “multiple members of Dr. Tessier-Lavigne’s labs over the years appear to have manipulated research data and/or fallen short of accepted scientific practices” and pointed to “the culture of the lab” as a key factor (p. 5). To date three papers co-authored by Tessier-Lavigne (two published in Science and one in Cell) have been retracted, and according to a statement on the Tessier-Lavigne lab website, he is pursuing “robust” and “thorough” corrections to two papers published in Nature. Tessier-Lavigne resigned as Stanford University president effective August 31.

One way labs can establish a culture of ethical and reproducible practices is to create a lab manual. Manual form and content can vary, but common elements include:

  • A mission and values statement
  • Expectations of lab members and code of conduct
  • Available resources 
  • Policies and practices relating to communication; experimental protocols; data recording, analysis, and deposition; coding; and authorship and publication
  • Guidance for effective writing, figures, and presentations
  • Support for conferences and travel
  • Procedures for recommendation letter requests

Lab manuals can take many forms: websites, GitHub pages, Google docs, PDFs, and more. For descriptions, templates and examples, please see the resources below.

Descriptions and templates:

Aly describes how creating a lab manual saves time in the long run, makes it easier for lab members to find answers to common questions, and enhances transparency about roles and expectations.

Fay offers step-by-step instructions with screenshots for making an editable copy of the Faylab Lab Manual as a template (see the Examples section below for a link to the manual).

  • Kovacs M, et al. (2022). Lab manuals for efficient and high quality science in a happy and safe work environment [preprint]. MetaArXiv Preprints. doi: https://doi.org/10.31222/osf.io/bzcxg

In this preprint, Kovacs and co-authors provide a template and a web app to simplify the process of creating a lab manual. Sections fall under two broad categories, “Who we are” and “How we do things.”

Teplitzky, Deardorff and Borghi, members of the Bay Area Open Science Group, offer a template “as a resource for teams interested in having conversations about open science.” Sections cover authorship and collaboration, articles and research materials, data and code, and communication and impact.

Example lab manuals:

Covers expectations and responsibilities; code of conduct; lab resources; and general policies, including meetings, data management, Open Science, presentations, and recommendation letters.

Covers culture and conduct; communication and coordination; reproducibility practices; code style, practices, publication, repositories, and GitHub; working with big data; Unix commands and cluster computing; checklists; and resources.

  • Fay Lab (University of Massachusetts Dartmouth School for Marine Science and Technology): Faylab Lab Manual

The Fay Lab’s “book of magical secrets” covers lab culture and philosophy; code of conduct and expectations; onboarding and offboarding procedures; funding; communication; academics and courses; and resources. The manual was developed through the lab’s participation in the Openscapes Champions Program.

With playful banner illustrations and core lab values described by the acronym BEER AND TACOS, this manual employs humor in covering lab mission and values; communication and collaboration; lab notebooks and data deposition; reading, writing, publishing, and peer review; grants and fellowships; professional activities and development; resources; well-being; and conflicts of interest.

Figure 1. Fraser Lab Compact, Philosophy and Resources site banner. Accessed 19 September 2023 at https://fraserlab.com/philosophy/

Covers funding; roles and policies; communication; guidelines for scientific integrity and reproducibility; lab notebooks, computing, and backup; and recommendation letters. Includes an FAQ and glossary.

Covers expectations and roles; code of conduct; lab resources; general policies, including meetings, data management, presentations, and recommendation letters; funding; and undergraduate research.

If you support researchers who are seeking ways to encourage and codify scientific consistency and rigor in their labs, lab manuals can provide models and guidelines for transparent, open, and reproducible practices.

Elliott Smith, Emerging Technologies & Bioinformatics Librarian, University of California Berkeley

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