Fit for Nature methods

[jeromekelleher]

This topic gathers together some notes to see if the tskit paper would be a good fit as a Nature Methods article.

According to the aims and scope (selected quotes)

Nature Methods is a forum for the publication of novel methods and significant improvements to tried-and-tested basic research techniques in the life sciences.

The journal publishes method developments (Articles, Brief Communications), performance comparisons of related, established methods (Analyses), and collections of tools or datasets of broad interest (Resources) as primary research papers.

Specific areas of interest include, but are not limited to:

• Computational, statistical and machine learning methods for analysis, modeling and visualization of biological data

So I think tskit is firmly in scope here, although there's a question about whether this would be a "method development" or a "resource". I think it's probably best pitched as a resource as we're not putting forward anything new, more summarising the combined utility of a large number of different developments.

[jeromekelleher]

Some comparable papers published at Nature Methods:

• Scikit-bio: a fundamental Python library for biological omic data analysis (2025). https://www.nature.com/articles/s41592-025-02981-z
• SpatialData: an open and universal data framework for spatial omics (2025). https://www.nature.com/articles/s41592-025-02981-z
• PyImageJ: A library for integrating ImageJ and Python (2022). https://www.nature.com/articles/s41592-022-01655-4
• BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference (2025). https://www.nature.com/articles/s41592-025-02751-x
• Bioconda: sustainable and comprehensive software distribution for the life sciences (2018). https://www.nature.com/articles/s41592-018-0046-7

[jeromekelleher]

Regarding format, nearly all the papers listed above are either "Brief Communication" or "Correspondence". Given the unique position that tskit holds as a general purpose ARG library, I think this is likely the correct route here. Here's the description for the content types (from here:

Brief Communication

A Brief Communication is a concise report describing potentially groundbreaking yet preliminary method or tool developments, highly practical tweaks to an existing method or tool, software platforms, resources of broad interest, and technical critiques of widely used methodologies.

Format

• Abstract – up to 70 words, unreferenced.
• Main text – 1,200 words (up to 1600 words with editorial discretion), including abstract, references and figure legends.
• The main text should not contain sections nor subheadings.
• Display items – maximum 2 figures and/or tables (up to 3 items with editorial discretion).
• Online Methods section should be included and should contain subheadings.
• References – as a guideline, we typically recommend up to 20.
• Brief Communications include received/accepted dates.
• Brief Communications may be accompanied by supplementary information.
• Brief Communications are peer reviewed.

Correspondence

The Correspondence section provides a forum for brief announcements of broadly interesting tools, resources, initiatives, news, and opinions on issues relevant to the journal’s readership. Correspondence should not include new research data or analysis.

Format

• Main text – up to 800 words. No abstract or online Methods section is included.
• Display items – 1 figure or table.
• References – up to 10 references. Article titles are omitted from the reference list.
• Correspondence may be peer-reviewed at the editors’ discretion.
• Note that Correspondence pieces are not technical comments on peer-reviewed research papers; these should be submitted as Matters Arising.

[jeromekelleher]

Here's my take. The main purpose of this paper is

• to give credit to tskit developers
• to provide a citation for tskit itself
• outline the high-level purpose of tskit and its role as part of a distributed software ecosytem

These goals are well met by a minimal Correspondence article.

The algorithmic innovations that are incorporated into tskit are well documented elsewhere, and we can cite these. Going for a full Article style format would require significant extra work, needing substantial demonstrations of utility and comparisons against existing software. I don't see the point, to be honest --- scalability and benchmarking have been done elsewhere and it'll be a lot of work to recapitulate this, for, at the end of the day, basically the the same outcome as writing the 1200 word summary.

I'm going to have a go at writing the Correspondence version and see what it looks like.