Evidence map›Paper›PMID 38802733›Full record

ArticleBMC bioinformatics2024

SEDA 2024 update: enhancing the SEquence DAtaset builder for seamless integration into automated data analysis pipelines.

Miguel Reboiro-Jato, Daniel Pérez-Rodríguez, Miguel José Da Silva, David Vila-Fernández, Cristina P Vieira, Jorge Vieira, Hugo López-Fernández

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

7 authors.

Miguel Reboiro-JatoSING Research Group, SERGAS-UVIGO, Galicia Sur Health Research Institute (IIS Galicia Sur), 36213, Vigo, Spain.
Daniel Pérez-RodríguezNeuroEpigenetics Lab, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario de Santiago, 15706, Santiago de Compostela, Spain.
Miguel José Da SilvaSING Research Group, SERGAS-UVIGO, Galicia Sur Health Research Institute (IIS Galicia Sur), 36213, Vigo, Spain.
David Vila-FernándezSING Research Group, SERGAS-UVIGO, Galicia Sur Health Research Institute (IIS Galicia Sur), 36213, Vigo, Spain.
Cristina P VieiraInstituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
Jorge VieiraInstituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
Hugo López-FernándezSING Research Group, SERGAS-UVIGO, Galicia Sur Health Research Institute (IIS Galicia Sur), 36213, Vigo, Spain. hlfernandez@uvigo.gal.

Funding

Consellería de Educación, Universidades e Formación Profesional (Xunta de Galicia) ED431C 2022/03-GRCFundação para a Ciência e a Tecnologia UIDB/04293/2020Xunta de Galicia TR349V
6 · The paper itself

Abstract

backgroundThe initial version of SEDA assists life science researchers without programming skills with the preparation of DNA and protein sequence FASTA files for multiple bioinformatics applications. However, the initial version of SEDA lacks a command-line interface for more advanced users and does not allow the creation of automated analysis pipelines.

resultsThe present paper discusses the updates of the new SEDA release, including the addition of a complete command-line interface, new functionalities like gene annotation, a framework for automated pipelines, and improved integration in Linux environments.

conclusionSEDA is an open-source Java application and can be installed using the different distributions available ( https://www.sing-group.org/seda/download.html ) as well as through a Docker image ( https://hub.docker.com/r/pegi3s/seda ). It is released under a GPL-3.0 license, and its source code is publicly accessible on GitHub ( https://github.com/sing-group/seda ). The software version at the time of submission is archived at Zenodo (version v1.6.0, http://doi.org/10.5281/zenodo.10201605 ).

Indexed as

Computational BiologySoftwareData AnalysisDockerFASTAPipelinesReproducibilityWorkflows

Identifiers

PMID38802733
PMCPMC11131258

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.