ArticleGigaScience2019
SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Empowering bioinformatics communities with Nextflow and nf-core.Genome biology · 2025Review
- Predicting blood-brain barrier permeability of molecules with a large language model and machine learning.Scientific reports · 2024Article
- Modeling the impact of thoracic pressure on intracranial pressure.NPJ microgravity · 2024Article
- Design considerations for workflow management systems use in production genomics research and the clinic.Scientific reports · 2021Article
- Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers.Nature methods · 2021Review
- pyrpipe: a Python package for RNA-Seq workflows.NAR genomics and bioinformatics · 2021Article
- Compi: a framework for portable and reproducible pipelines.PeerJ. Computer science · 2021Article
- Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix.GigaScience · 2020Article
- MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets.Frontiers in genetics · 2020Article
- A Serverless Tool for Platform Agnostic Computational Experiment Management.Frontiers in neuroinformatics · 2019Article
- Predicting Off-Target Binding Profiles With Confidence Using Conformal Prediction.Frontiers in pharmacology · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe complex nature of biological data has driven the development of specialized software tools. Scientific workflow management systems simplify the assembly of such tools into pipelines, assist with job automation, and aid reproducibility of analyses. Many contemporary workflow tools are specialized or not designed for highly complex workflows, such as with nested loops, dynamic scheduling, and parametrization, which is common in, e.g., machine learning.
findingsSciPipe is a workflow programming library implemented in the programming language Go, for managing complex and dynamic pipelines in bioinformatics, cheminformatics, and other fields. SciPipe helps in particular with workflow constructs common in machine learning, such as extensive branching, parameter sweeps, and dynamic scheduling and parametrization of downstream tasks. SciPipe builds on flow-based programming principles to support agile development of workflows based on a library of self-contained, reusable components. It supports running subsets of workflows for improved iterative development and provides a data-centric audit logging feature that saves a full audit trace for every output file of a workflow, which can be converted to other formats such as HTML, TeX, and PDF on demand. The utility of SciPipe is demonstrated with a machine learning pipeline, a genomics, and a transcriptomics pipeline.
conclusionsSciPipe provides a solution for agile development of complex and dynamic pipelines, especially in machine learning, through a flexible application programming interface suitable for scientists used to programming or scripting.
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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.