Evidence map›Paper›PMID 32214318›Full record

ArticlePLoS computational biology2020

Ten simple rules for providing effective bioinformatics research support.

Judit Kumuthini, Michael Chimenti, Sven Nahnsen, Alexander Peltzer, Rebone Meraba, Ross McFadyen, Gordon Wells, Deanne Taylor, Mark Maienschein-Cline, Jian-Liang Li and 3 more

Abstract readEditorial
In one paragraph

Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing 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

17 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Review
  6. Review
  7. Article
  8. Article
  9. Review
  10. Article
  11. Article
  12. Article
  13. Article
  14. Review
  15. Article
  16. Article
  17. Haemoprotozoan surveillance in peri-urban native and introduced wildlife from Australia.Current research in parasitology & vector-borne diseases · 2021
    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

13 authors.

Judit KumuthiniH3ABioNet, Centre for Proteomic and Genomic Research, Cape Town, South Africa.
Michael ChimentiIowa Institute of Human Genetics, Bioinformatics Division, Carver College of Medicine, University of Iowa, Iowa City, United States of America.ORCID 0000-0002-4433-9976
Sven NahnsenQuantitative Biology Centre, Eberhard Karls University of Tübingen, Tübingen, Baden-Württemberg, Germany.
Alexander PeltzerQuantitative Biology Centre, Eberhard Karls University of Tübingen, Tübingen, Baden-Württemberg, Germany.ORCID 0000-0002-6503-2180
Rebone MerabaH3ABioNet, Centre for Proteomic and Genomic Research, Cape Town, South Africa.
Ross McFadyenH3ABioNet, Centre for Proteomic and Genomic Research, Cape Town, South Africa.
Gordon WellsH3ABioNet, Centre for Proteomic and Genomic Research, Cape Town, South Africa.
Deanne TaylorDepartment of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.ORCID 0000-0002-3302-4610
Mark Maienschein-ClineResearch Informatics Core, University of Illinois at Chicago, Chicago, Illinois, United States of America.
Jian-Liang LiIntegrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Durham, North Carolina, United States of America.ORCID 0000-0002-6487-081X
Jyothi ThimmapuramBioinformatics Core, Purdue University, West Lafayette, Indiana, United States of America.ORCID 0000-0002-2437-5734
Radha Murthy-KaruturiDepartment of Computational Sciences, The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America.ORCID 0000-0001-5217-756X
Lyndon ZassH3ABioNet, Centre for Proteomic and Genomic Research, Cape Town, South Africa.

Funding

H3ABioNet: a sustainable African Bioinformatics Network for H3AfricaU41HG006941 · NHGRI · UNIVERSITY OF CAPE TOWN · PI MULDER, NICOLA · 2012 to 2017
$14.8M
NHGRI NIH HHS U41 HG006941
6 · The paper itself

Abstract

Life scientists are increasingly turning to high-throughput sequencing technologies in their research programs, owing to the enormous potential of these methods. In a parallel manner, the number of core facilities that provide bioinformatics support are also increasing. Notably, the generation of complex large datasets has necessitated the development of bioinformatics support core facilities that aid laboratory scientists with cost-effective and efficient data management, analysis, and interpretation. In this article, we address the challenges-related to communication, good laboratory practice, and data handling-that may be encountered in core support facilities when providing bioinformatics support, drawing on our own experiences working as support bioinformaticians on multidisciplinary research projects. Most importantly, the article proposes a list of guidelines that outline how these challenges can be preemptively avoided and effectively managed to increase the value of outputs to the end user, covering the entire research project lifecycle, including experimental design, data analysis, and management (i.e., sharing and storage). In addition, we highlight the importance of clear and transparent communication, comprehensive preparation, appropriate handling of samples and data using monitoring systems, and the employment of appropriate tools and standard operating procedures to provide effective bioinformatics support.

Indexed as

Biomedical ResearchCommunicationComputational BiologyHigh-Throughput Nucleotide SequencingHumansResearch Design

Identifiers

PMID32214318
PMCPMC7098546

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.