ArticleGigaScience2025
Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology.
Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
7 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Software Tools for Passive Acoustic Monitoring in Aquatic and Terrestrial Bio- and Ecoacoustics: A Living Systematic Review.F1000Research · 2026Pooled it
- Introducing GalaxyR: an easy-to-use R implementation of the Galaxy API.BMC bioinformatics · 2026Article
- Article
- Galaxy for accessible, reproducible, and collaborative data analyses: 2026 update.Nucleic acids research · 2026Article
- Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data.bioRxiv : the preprint server for biology · 2025Article
- Biodiversity science and biosurveillance are fellow travelers.Bioscience · 2025Article
- Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology.GigaScience · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
30 authors.
Funding
Abstract
Numerous conceptual frameworks exist for best practices in research data and analysis (e.g., Open Science and FAIR principles). In practice, there is a need for further progress to improve transparency, reproducibility, and confidence in ecology. Here, we propose a practical and operational framework for researchers and experts in ecology to achieve best practices for building analytical procedures from individual research projects to production-level analytical pipelines. We introduce the concept of atomization to identify analytical steps that support generalization by allowing us to go beyond single analyses. The term atomization is employed to convey the idea of single analytical steps as "atoms" composing an analytical procedure. When generalized, "atoms" can be used in more than a single case analysis. These guidelines were established during the development of the Galaxy-Ecology initiative, a web platform dedicated to data analysis in ecology. Galaxy-Ecology allows us to demonstrate a way to reach higher levels of reproducibility in ecological sciences by increasing the accessibility and reusability of analytical workflows once atomized and generalized.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.