ArticleBioinformatics (Oxford, England)2016
AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.
Article in Bioinformatics (Oxford, England), 2016. 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.
- Democratizing bioinformatics through easily accessible software platforms for non-experts in the field.BioTechniques · 2022Article
- ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp.PLoS neglected tropical diseases · 2019Article
- Article
- From command-line bioinformatics to bioGUI.PeerJ · 2019Article
- Implementation of informatics for integrating biology and the bedside (i2b2) platform as Docker containers.BMC medical informatics and decision making · 2018Article
- The Scientific Filesystem.GigaScience · 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
- Nextflow enables reproducible computational workflows.Nature biotechnology · 2017Article
- Article
- Article
- Singularity: Scientific containers for mobility of compute.PloS one · 2017Article
- 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
motivationThere is a growing need in bioinformatics for easy-to-use software implementations of algorithms that are usable across platforms. At the same time, reproducibility of computational results is critical and often a challenge due to source code changes over time and dependencies.
resultsThe approach introduced in this paper addresses both of these needs with AlgoRun, a dedicated packaging system for implemented algorithms, using Docker technology. Implemented algorithms, packaged with AlgoRun, can be executed through a user-friendly interface directly from a web browser or via a standardized RESTful web API to allow easy integration into more complex workflows. The packaged algorithm includes the entire software execution environment, thereby eliminating the common problem of software dependencies and the irreproducibility of computations over time. AlgoRun-packaged algorithms can be published on http://algorun.org, a centralized searchable directory to find existing AlgoRun-packaged algorithms. AVAILABILITY AND IMPLEMENTATION: AlgoRun is available at http://algorun.org and the source code under GPL license is available at https://github.com/algorun CONTACT: laubenbacher@uchc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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.