Evidence map›Paper›PMID 35259087›Full record

ArticleMicrobial genomics2022

Software testing in microbial bioinformatics: a call to action.

Boas C L van der Putten, C I Mendes, Brooke M Talbot, Jolinda de Korne-Elenbaas, Rafael Mamede, Pedro Vila-Cerqueira, Luis Pedro Coelho, Christopher A Gulvik, Lee S Katz, The Asm Ngs Hackathon Participants

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbial genomics, 2022. 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. 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

10 authors.

Boas C L van der PuttenDepartment of Medical Microbiology, Amsterdam UMC, University of Amsterdam, the Netherlands.
C I MendesInstituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
Brooke M TalbotDepartment of Biological and Biomedical Sciences, Emory University, Atlanta, GA, USA.
Jolinda de Korne-ElenbaasDepartment of Medical Microbiology, Amsterdam UMC, University of Amsterdam, the Netherlands.
Rafael MamedeInstituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
Pedro Vila-CerqueiraInstituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
Luis Pedro CoelhoInstitute of Science and Technology for Brain-Inspired Intelligence, Fudan University, PR China.
Christopher A GulvikBacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Lee S KatzCenter for Food Safety, University of Georgia, Griffin, GA, USA.
The Asm Ngs Hackathon Participants

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Computational algorithms have become an essential component of research, with great efforts by the scientific community to raise standards on development and distribution of code. Despite these efforts, sustainability and reproducibility are major issues since continued validation through software testing is still not a widely adopted practice. Here, we report seven recommendations that help researchers implement software testing in microbial bioinformatics. We have developed these recommendations based on our experience from a collaborative hackathon organised prior to the American Society for Microbiology Next Generation Sequencing (ASM NGS) 2020 conference. We also present a repository hosting examples and guidelines for testing, available from https://github.com/microbinfie-hackathon2020/CSIS.

Indexed as

Computational BiologySoftwareAlgorithmsHigh-Throughput Nucleotide SequencingReproducibility of ResultsUnited Statescomputational biologycontinuous integrationsoftware testing

Identifiers

PMID35259087
PMCPMC9176277

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.