Evidence map›Paper›PMID 25960870›Full record

ArticleGigaScience2015

BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ.

Anthony Bretaudeau, Cyril Monjeaud, Yvan Le Bras, Fabrice Legeai, Olivier Collin

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in GigaScience, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
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

2 citing papers in PubMed.

  1. blend4php: a PHP API for galaxy.Database : the journal of biological databases and curation · 2017
    Article
  2. 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

5 authors.

Anthony BretaudeauINRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, 35042 France ; INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042 France.
Cyril MonjeaudINRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042 France.
Yvan Le BrasINRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042 France.
Fabrice LegeaiINRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, 35042 France ; INRIA, IRISA, GenScale, Campus de Beaulieu, Rennes, 35042 France.
Olivier CollinINRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042 France.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundMany bioinformatics tools use reference data, such as genome assemblies or sequence databanks. Galaxy offers multiple ways to give access to this data through its web interface. However, the process of adding new reference data was customarily manual and time consuming, even more so when this data needed to be indexed in a variety of formats (e.g. Blast, Bowtie, BWA, or 2bit). BioMAJ is a widely used and stable software that is designed to automate the download and transformation of data from various sources. This data can be used directly from the command line, in more complex systems, such as Mobyle, or by using a REST API.

findingsTo ease the process of giving access to reference data in Galaxy, we have developed the BioMAJ2Galaxy module, which enables the gap between BioMAJ and Galaxy to be bridged. With this module, it is now possible to configure BioMAJ to automatically download some reference data, to then convert and/or index it in various formats, and then make this data available in a Galaxy server using data libraries or data managers.

conclusionsThe developments presented in this paper allow us to integrate the reference data in Galaxy in an automatic, reliable, and diskspace-saving way. The code is freely available on the GenOuest GitHub account (https://github.com/genouest/biomaj2galaxy).

Indexed as

Computational BiologyInternetUser-Computer InterfaceAutomationBioMAJData librariesData managerGalaxyReference data

Identifiers

PMID25960870
PMCPMC4425870

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.