SynthesisNature protocols2024
Packaging and containerization of computational methods.
Synthesis in Nature protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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
12 citing papers in PubMed.
- Quality assessment and control of unprocessed anatomical, functional and diffusion MRI of the human brain using MRIQC.Nature protocols · 2026Review
- Enhancing reproducibility in neuroimaging with containerized archival.Brain imaging and behavior · 2026Article
- Review
- Article
- Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines.PLoS computational biology · 2025Article
- Autonomous Self-Evolving Research on Biomedical Data: The DREAM Paradigm.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Advantages of Software Containerization in Public Health Infectious Disease Genomic Surveillance.Emerging infectious diseases · 2025Article
- Guidance for sharing computational models of neural stimulation: from project planning to publication.Journal of neural engineering · 2025Review
- Taming large-scale genomic analyses via sparsified genomics.Nature communications · 2025Article
- Mars: simplifying bioinformatics workflows through a containerized approach to tool integration and management.Bioinformatics advances · 2025Article
- A how-to guide for code sharing in biology.PLoS biology · 2024Review
- Genomic reproducibility in the bioinformatics era.Genome biology · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
20 authors.
Funding
Abstract
Methods for analyzing the full complement of a biomolecule type, e.g., proteomics or metabolomics, generate large amounts of complex data. The software tools used to analyze omics data have reshaped the landscape of modern biology and become an essential component of biomedical research. These tools are themselves quite complex and often require the installation of other supporting software, libraries and/or databases. A researcher may also be using multiple different tools that require different versions of the same supporting materials. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging and containerization are different approaches to satisfy this need by delivering omics tools already wrapped in additional software that makes the tools easier to install and use. In this systematic review, we describe and compare the features of prominent packaging and containerization platforms. We outline the challenges, advantages and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers and system administrators. We also propose principles to make the distribution of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.
Indexed as
Identifiers
38565959What 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.