ArticleF1000Research2022
Sapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformatics.
Article in F1000Research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Managing workflow executions with WESkit.Bioinformatics (Oxford, England) · 2026Article
- WorkflowHub: a registry for computational workflows.Scientific data · 2025Article
- Application of mindfulness-based stress reduction plan in post-stroke patients with mild depression.Frontiers in neurology · 2025Article
- DDBJ update in 2023: the MetaboBank for metabolomics data and associated metadata.Nucleic acids research · 2024Article
- Recording provenance of workflow runs with RO-Crate.PloS one · 2024Article
- DNA Data Bank of Japan (DDBJ) update report 2022.Nucleic acids research · 2023Article
- A workflow reproducibility scale for automatic validation of biological interpretation results.GigaScience · 2022Article
- Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows.GigaScience · 2022Article
- The NBDC-DDBJ imputation server facilitates the use of controlled access reference panel datasets in Japan.Human genome variation · 2022Article
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The increased demand for efficient computation in data analysis encourages researchers in biomedical science to use workflow systems. Workflow systems, or so-called workflow languages, are used for the description and execution of a set of data analysis steps. Workflow systems increase the productivity of researchers, specifically in fields that use high-throughput DNA sequencing applications, where scalable computation is required. As systems have improved the portability of data analysis workflows, research communities are able to share workflows to reduce the cost of building ordinary analysis procedures. However, having multiple workflow systems in a research field has resulted in the distribution of efforts across different workflow system communities. As each workflow system has its unique characteristics, it is not feasible to learn every single system in order to use publicly shared workflows. Thus, we developed Sapporo, an application to provide a unified layer of workflow execution upon the differences of various workflow systems. Sapporo has two components: an application programming interface (API) that receives the request of a workflow run and a browser-based client for the API. The API follows the Workflow Execution Service API standard proposed by the Global Alliance for Genomics and Health. The current implementation supports the execution of workflows in four languages: Common Workflow Language, Workflow Description Language, Snakemake, and Nextflow. With its extensible and scalable design, Sapporo can support the research community in utilizing valuable resources for data analysis.
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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.