ArticlePloS one2016
GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- Shennong: A Python toolbox for audio speech features extraction.Behavior research methods · 2023Article
- Cloud-enabled Biodepot workflow builder integrates image processing using Fiji with reproducible data analysis using Jupyter notebooks.Scientific reports · 2022Article
- Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features.Journal of cheminformatics · 2022Article
- Democratizing bioinformatics through easily accessible software platforms for non-experts in the field.BioTechniques · 2022Article
- A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research.Metabolites · 2022Review
- Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data.BMC bioinformatics · 2020Article
- A Guide and Toolbox to Replicability and Open Science in Entomology.Journal of insect science (Online) · 2020Review
- Building Containerized Workflows Using the BioDepot-Workflow-Builder.Cell systems · 2019Article
- ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp.PLoS neglected tropical diseases · 2019Article
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- Article
- Implementation of informatics for integrating biology and the bedside (i2b2) platform as Docker containers.BMC medical informatics and decision making · 2018Article
- Reproducible Bioconductor workflows using browser-based interactive notebooks and containers.Journal of the American Medical Informatics Association : JAMIA · 2018Article
- Bio-Docklets: virtualization containers for single-step execution of NGS pipelines.GigaScience · 2017Article
- Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform.Journal of integrative bioinformatics · 2017Article
- GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software.GigaScience · 2017Article
- Article
- Expression, Localization of SUMO-1, and Analyses of Potential SUMOylated Proteins inFrontiers in physiology · 2017Article
- Use of application containers and workflows for genomic data analysis.Journal of pathology informatics · 2016Article
- Successes and Struggles with Computational Reproducibility: Lessons from the Fragile Families Challenge.Socius : sociological research for a dynamic worldArticle
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
Abstract
Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.
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.