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Peer-Review Record

Keep It Simple: Using README Files to Advance Standardization in Chronobiology

Clocks & Sleep 2023, 5(3), 499-506;
by Tomasz Zieliński 1,*, James J. L. Hodge 2 and Andrew J. Millar 1
Reviewer 1:
Clocks & Sleep 2023, 5(3), 499-506;
Submission received: 19 July 2023 / Revised: 25 August 2023 / Accepted: 28 August 2023 / Published: 30 August 2023
(This article belongs to the Special Issue Reproducibility in Sleep and Circadian Science)

Round 1

Reviewer 1 Report

The manuscript presents an approach towards standardization in chronobiology through the use of README templates. Overall, the clarity of the content is satisfactory, but some sections require further elaboration and examples to strengthen the arguments. 


The idea is relevant, but it does not address how to motivate researchers to prepare a README file for their research. Creating a specific repository for chronobiological research, similar to BioModels for systems biology models, might be a more effective solution.

The authors should investigate why current circadian and sleep repositories (e.g., [26] and [29]) do not ensure FAIR principles in chronobiology and propose potential solutions for improvement.

Additionally, the manuscript lacks examples of different methods and protocols used in circadian research and the reproducibility issues they might cause. For instance, the authors could discuss various computational methods for identifying and characterizing rhythmic responses (e.g., see 10.1177/0748730410379711, 10.1177/0748730418789536, 10.1186/s12859-020-03830-w, 10.1007/978-1-0716-2249-0_3) and address/discuss the reproducibility challenges associated with employing these methods (e.g., see 10.1093/bib/bbaa135).

To support the proposed work, the authors could explore the development of a computational tool capable of assessing the reproducibility of a study based on its provided metadata.

Furthermore, establishing a dedicated repository for depositing metadata related to circadian research, accompanied by specific descriptors to enhance reproducibility, could be discussed.

The manuscript should identify and discuss the minimal descriptors required to enhance reproducibility in the field of chronobiology. These descriptors should be listed, explained, and demonstrated (evaluated) through a specific example.

The use of multiple templates may hinder standardization, which contradicts the research's goals. Instead, the authors should define a minimal set of descriptors applicable to all organisms.


Line 77: Move the reference [19] before the full stop.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

The article provides a comprehensive overview of the significance of standardization, particularly in the context of biomedical research data. The emphasis on metadata standards as a foundation for the FAIR principles is aptly highlighted, acknowledging their role in facilitating data discovery, comprehension, and reusability.

The article effectively identifies the existing barriers to widespread adoption of metadata standards in biological research. These barriers, ranging from complexity and lack of incentives to technical challenges and resistance to change, resonate with the challenges faced by the scientific community in implementing standardized practices.

The unique challenges faced by standardization in the field of chronobiology are well-articulated, specifically the complexities arising from longitudinal data, diverse model organisms, and varied measurement techniques. The proposal of an approach centered on simplicity and practicality through the development of tailored README templates for specific data types and species is really interesting and usefull, in order to mitigate challenges and encourage broader participation from the scientific public.

In conclusion, the article effectively communicates the importance of standardization in biomedical research data and outlines a promising approach to address the challenges. I would suggest the authors to describe in extent the major errors implied by using different not standardized reports in chronobiology vs the great advances that will be registered after the implementation of the proposed solution. The call for collaboration and contribution serves to engage potential stakeholders in this important endeavor. It would be beneficial to further elaborate on the potential impact of the proposed README templates and how they could potentially overcome the identified barriers in the field of chronobiology. 


Author Response

Please see the attachment

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

The authors have addressed my concerns.

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