ArticleBiology direct2015
Experiences with workflows for automating data-intensive bioinformatics.
Article in Biology direct, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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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.
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Who cites it
21 citing papers in PubMed.
- Integrated data-driven biotechnology research environments.Database : the journal of biological databases and curation · 2025Review
- The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more.PeerJ · 2025Article
- Novel multi-cluster workflow system to support real-time HPC-enabled epidemic science: Investigating the impact of vaccine acceptance on COVID-19 spread.Journal of parallel and distributed computing · 2024Article
- Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems.Computational and structural biotechnology journal · 2023Review
- An update on immunological and molecular tests and their impact in infectious uveitis.Frontiers in ophthalmology · 2023Review
- Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.Wiley interdisciplinary reviews. Computational molecular science · 2022Article
- Identifying Opportunities for Workflow Automation in Health Care: Lessons Learned from Other Industries.Applied clinical informatics · 2021Review
- Arteria: An automation system for a sequencing core facility.GigaScience · 2019Article
- Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv.GigaScience · 2019Article
- Single-cell technologies in reproductive immunology.American journal of reproductive immunology (New York, N.Y. : 1989) · 2019Review
- SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines.GigaScience · 2019Article
- Script of Scripts: A pragmatic workflow system for daily computational research.PLoS computational biology · 2019Article
- Managing genomic variant calling workflows with Swift/T.PloS one · 2019Article
- Enabling precision medicine via standard communication of HTS provenance, analysis, and results.PLoS biology · 2018Article
- Improving data workflow systems with cloud services and use of open data for bioinformatics research.Briefings in bioinformatics · 2018Review
- Article
- Kronos: a workflow assembler for genome analytics and informatics.GigaScience · 2017Article
- A review of bioinformatic pipeline frameworks.Briefings in bioinformatics · 2017Review
- Recommendations on e-infrastructures for next-generation sequencing.GigaScience · 2016Review
- Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles.Journal of cheminformatics · 2016Article
Corrections and comments
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Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources and carry out data management and analysis tasks on large scale. Workflow systems can be useful to simplify construction of analysis pipelines that automate tasks, support reproducibility and provide measures for fault-tolerance. However, workflow systems can incur significant development and administration overhead so bioinformatics pipelines are often still built without them. We present the experiences with workflows and workflow systems within the bioinformatics community participating in a series of hackathons and workshops of the EU COST action SeqAhead. The organizations are working on similar problems, but we have addressed them with different strategies and solutions. This fragmentation of efforts is inefficient and leads to redundant and incompatible solutions. Based on our experiences we define a set of recommendations for future systems to enable efficient yet simple bioinformatics workflow construction and execution.
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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.