ArticlePeerJ. Computer science2021
Compi: a framework for portable and reproducible pipelines.
Article in PeerJ. Computer science, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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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
6 citing papers in PubMed.
- Software engineering for reproducible pipeline development in bioinformatics.Frontiers in bioinformatics · 2026Review
- SEDA 2024 update: enhancing the SEquence DAtaset builder for seamless integration into automated data analysis pipelines.BMC bioinformatics · 2024Article
- Optical diagnosis in still images of colorectal polyps: comparison between expert endoscopists and PolyDeep, a Computer-Aided Diagnosis system.Frontiers in oncology · 2024Article
- MyBrain-Seq: A Pipeline for MiRNA-Seq Data Analysis in Neuropsychiatric Disorders.Biomedicines · 2023Article
- Negative Samples for Improving Object Detection-A Case Study in AI-Assisted Colonoscopy for Polyp Detection.Diagnostics (Basel, Switzerland) · 2023Article
- Performance of Convolutional Neural Networks for Polyp Localization on Public Colonoscopy Image Datasets.Diagnostics (Basel, Switzerland) · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Compi is an application framework to develop end-user, pipeline-based applications with a primary emphasis on: (i) user interface generation, by automatically generating a command-line interface based on the pipeline specific parameter definitions; (ii) application packaging, with compi-dk, which is a version-control-friendly tool to package the pipeline application and its dependencies into a Docker image; and (iii) application distribution provided through a public repository of Compi pipelines, named Compi Hub, which allows users to discover, browse and reuse them easily. By addressing these three aspects, Compi goes beyond traditional workflow engines, having been specially designed for researchers who want to take advantage of common workflow engine features (such as automatic job scheduling or logging, among others) while keeping the simplicity and readability of shell scripts without the need to learn a new programming language. Here we discuss the design of various pipelines developed with Compi to describe its main functionalities, as well as to highlight the similarities and differences with similar tools that are available. An open-source distribution under the Apache 2.0 License is available from GitHub (available at https://github.com/sing-group/compi). Documentation and installers are available from https://www.sing-group.org/compi. A specific repository for Compi pipelines is available from Compi Hub (available at https://www.sing-group.org/compihub.
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.