ArticleBriefings in bioinformatics2015
Virtual Reference Environments: a simple way to make research reproducible.
Article in Briefings in bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed.
- The five pillars of computational reproducibility: bioinformatics and beyond.Briefings in bioinformatics · 2023Article
- Development and Validation of an Inflammatory Response-Related Gene Signature for Predicting the Prognosis of Pancreatic Adenocarcinoma.Inflammation · 2022Article
- Analysing and simulating energy-based models in biology using BondGraphTools.The European physical journal. E, Soft matter · 2021Article
- Hierarchical semantic composition of biosimulation models using bond graphs.PLoS computational biology · 2021Article
- Towards reproducible computational drug discovery.Journal of cheminformatics · 2020Review
- Energy-based analysis of biomolecular pathways.Proceedings. Mathematical, physical, and engineering sciences · 2017Article
- A review of bioinformatic pipeline frameworks.Briefings in bioinformatics · 2017Review
- Methods for enhancing the reproducibility of biomedical research findings using electronic health records.BioData mining · 2017Review
- Systems analysis identifies miR-29b regulation of invasiveness in melanoma.Molecular cancer · 2016Article
- Tools and techniques for computational reproducibility.GigaScience · 2016Review
- Modelling the conditional regulatory activity of methylated and bivalent promoters.Epigenetics & chromatin · 2015Article
- Spatially transformed fluorescence image data for ERK-MAPK and selected proteins within human epidermis.GigaScience · 2015Article
- FlexDM: Simple, parallel and fault-tolerant data mining using WEKA.Source code for biology and medicine · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
'Reproducible research' has received increasing attention over the past few years as bioinformatics and computational biology methodologies become more complex. Although reproducible research is progressing in several valuable ways, we suggest that recent increases in internet bandwidth and disk space, along with the availability of open-source and free-software licences for tools, enable another simple step to make research reproducible. In this article, we urge the creation of minimal virtual reference environments implementing all the tools necessary to reproduce a result, as a standard part of publication. We address potential problems with this approach, and show an example environment from our own work.
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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.