Evidence map›Paper›PMID 24907367›Full record

ArticleBioinformatics (Oxford, England)2014

MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure.

Jihoon Kim, Eric Levy, Alex Ferbrache, Petra Stepanowsky, Claudiu Farcas, Shuang Wang, Stefan Brunner, Tyler Bath, Yuan Wu, Lucila Ohno-Machado

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
1.6field-weighted citation impact, top 18% of its field
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed, 26 citations in OpenAlex.

  1. MicroRNAs Regulating Autophagy in Neurodegeneration.Advances in experimental medicine and biology · 2021
    Article
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  10. Oasis: online analysis of small RNA deep sequencing data.Bioinformatics (Oxford, England) · 2015
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 2 institutions in 2 countries.

Jihoon KimDivision of Biomedical Informatics, University of California at San Diego, Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA, Biomedical Informatics Program, School of Informatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria and Department of Biostatistics and Biomedical Informatics, Duke University, Durham, NC 27710, USA.
Eric LevyDivision of Biomedical Informatics, University of California at San Diego, Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA, Biomedical Informatics Program, School of Informatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria and Department of Biostatistics and Biomedical Informatics, Duke University, Durham, NC 27710, USA.
Alex FerbracheDivision of Biomedical Informatics, University of California at San Diego, Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA, Biomedical Informatics Program, School of Informatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria and Department of Biostatistics and Biomedical Informatics, Duke University, Durham, NC 27710, USA Division of Biomedical Informatics, University of California at San Diego, Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA, Biomedical Informatics Program, School of Informatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria and Department of Biostatistics and Biomedical Informatics, Duke University, Durham, NC 27710, USA.
Petra StepanowskyDivision of Biomedical Informatics, University of California at San Diego, Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA, Biomedical Informatics Program, School of Informatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria and Department of Biostatistics and Biomedical Informatics, Duke University, Durham, NC 27710, USA.
Claudiu FarcasDivision of Biomedical Informatics, University of California at San Diego, Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA, Biomedical Informatics Program, School of Informatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria and Department of Biostatistics and Biomedical Informatics, Duke University, Durham, NC 27710, USA.
Shuang WangDivision of Biomedical Informatics, University of California at San Diego, Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA, Biomedical Informatics Program, School of Informatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria and Department of Biostatistics and Biomedical Informatics, Duke University, Durham, NC 27710, USA.
Stefan BrunnerDivision of Biomedical Informatics, University of California at San Diego, Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA, Biomedical Informatics Program, School of Informatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria and Department of Biostatistics and Biomedical Informatics, Duke University, Durham, NC 27710, USA.
Tyler BathDivision of Biomedical Informatics, University of California at San Diego, Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA, Biomedical Informatics Program, School of Informatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria and Department of Biostatistics and Biomedical Informatics, Duke University, Durham, NC 27710, USA Division of Biomedical Informatics, University of California at San Diego, Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA, Biomedical Informatics Program, School of Informatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria and Department of Biostatistics and Biomedical Informatics, Duke University, Durham, NC 27710, USA.
Yuan WuDivision of Biomedical Informatics, University of California at San Diego, Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA, Biomedical Informatics Program, School of Informatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria and Department of Biostatistics and Biomedical Informatics, Duke University, Durham, NC 27710, USA.
Lucila Ohno-MachadoDivision of Biomedical Informatics, University of California at San Diego, Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA, Biomedical Informatics Program, School of Informatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria and Department of Biostatistics and Biomedical Informatics, Duke University, Durham, NC 27710, USA.
University of Applied Sciences Upper Austria · ATDuke University · US

Funding

iDASH: Integrating Data for Analysis, Anonymization, and SharingU54HL108460 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI OHNO-MACHADO, LUCILA · 2010 to 2015
$19.1M
San Diego Biomedical Informatics Education & Research (SABER)T15LM011271 · NLM · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SHAMIM NEMATI · 2012 to 2026
$9.7M
NHLBI NIH HHS U54HL108460NLM NIH HHS T15 LM011271
6 · The paper itself

Abstract

summaryMAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit (GPU) infrastructure. Using just a browser, users have access to results as web reports in just a few hours->600% end-to-end performance improvement over state of the art. MAGI's salient features are (i) transfer of large input files in native FASTA with Qualities (FASTQ) format through drag-and-drop operations, (ii) rapid prediction of microRNA target genes leveraging parallel computing with GPU devices, (iii) all-in-one analytics with novel feature extraction, statistical test for differential expression and diagnostic plot generation for quality control and (iv) interactive visualization and exploration of results in web reports that are readily available for publication. AVAILABILITY AND IMPLEMENTATION: MAGI relies on the Node.js JavaScript framework, along with NVIDIA CUDA C, PHP: Hypertext Preprocessor (PHP), Perl and R. It is freely available at http://magi.ucsd.edu.

Indexed as

Computer GraphicsSequence Analysis, RNAComputational BiologyInternetMicroRNAsProgramming LanguagesSoftwareMicroRNAs

Identifiers

PMID24907367
PMCPMC4173015
OpenAlexW2148311385

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

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.