ArticleBMC bioinformatics2017
Investigating reproducibility and tracking provenance - A genomic workflow case study.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 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
37 citing papers in PubMed.
- Trustworthy Agentic AI in Bioinformatics: From Workflow Automation to Traceable and Validated Biological Inference.Biology · 2026Review
- Reducing bulky medical images via shape-texture decoupled deep neural networks.Nature communications · 2026Article
- Architectural good practices for reproducible benchmarking in protein machine learning.Frontiers in bioinformatics · 2026Article
- TaxaScope: a container-native, visualization-centric workstation for genome-based bacterial taxonomy.Frontiers in microbiology · 2026Article
- g.nome, A Transparent Bioinformatics Pipeline that Enables Differential Expression and Alternative Splicing Analysis by Non-Computational Biologists.bioRxiv : the preprint server for biology · 2025Article
- Applying the FAIR Principles to computational workflows.Scientific data · 2025Article
- A standards perspective on genomic data reusability and reproducibility.Frontiers in bioinformatics · 2025Article
- Implementation of FAIR Practices in Computational Metabolomics Workflows-A Case Study.Metabolites · 2024Article
- Cancer treatment comes to age: from one-size-fits-all to next-generation sequencing (NGS) technologies.BioImpacts : BI · 2024Review
- An Automated Workflow Composition System for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing.Journal of the American Society for Mass Spectrometry · 2023Article
- Data Provenance in Biomedical Research: Scoping Review.Journal of medical Internet research · 2023Article
- PEGR: a flexible management platform for reproducible epigenomic and genomic research.Genome biology · 2022Article
- RESCRIPt: Reproducible sequence taxonomy reference database management.PLoS computational biology · 2021Article
- Orchestrating and sharing large multimodal data for transparent and reproducible research.Nature communications · 2021Article
- Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers.Nature methods · 2021Review
- RepeatFS: a file system providing reproducibility through provenance and automation.Bioinformatics (Oxford, England) · 2021Article
- Bioinformatics tools developed to support BioCompute Objects.Database : the journal of biological databases and curation · 2021Article
- Requirements and reliability of AI in the medical context.Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB) · 2021Review
- Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota.Microbiome · 2021Article
- Evaluation of serverless computing for scalable execution of a joint variant calling workflow.PloS one · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundComputational bioinformatics workflows are extensively used to analyse genomics data, with different approaches available to support implementation and execution of these workflows. Reproducibility is one of the core principles for any scientific workflow and remains a challenge, which is not fully addressed. This is due to incomplete understanding of reproducibility requirements and assumptions of workflow definition approaches. Provenance information should be tracked and used to capture all these requirements supporting reusability of existing workflows.
resultsWe have implemented a complex but widely deployed bioinformatics workflow using three representative approaches to workflow definition and execution. Through implementation, we identified assumptions implicit in these approaches that ultimately produce insufficient documentation of workflow requirements resulting in failed execution of the workflow. This study proposes a set of recommendations that aims to mitigate these assumptions and guides the scientific community to accomplish reproducible science, hence addressing reproducibility crisis.
conclusionsReproducing, adapting or even repeating a bioinformatics workflow in any environment requires substantial technical knowledge of the workflow execution environment, resolving analysis assumptions and rigorous compliance with reproducibility requirements. Towards these goals, we propose conclusive recommendations that along with an explicit declaration of workflow specification would result in enhanced reproducibility of computational genomic analyses.
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.