Evidence map›Paper›PMID 30134911›Full record

ArticleBMC bioinformatics2018

bioSyntax: syntax highlighting for computational biology.

Artem Babaian, Anicet Ebou, Alyssa Fegen, Ho Yin Kam, German E Novakovsky, Jasper Wong, Dylan Aïssi, Li Yao

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Templates for writing PyMOL scripts.Protein science : a publication of the Protein Society · 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

8 authors.

Artem BabaianTerry Fox Laboratory, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada. ababaian@bccrc.ca.ORCID http://orcid.org/0000-0002-4315-6262
Anicet EbouDepartement de Formation et de Recherches Agriculture et Ressources Animales, Institut National Polytechnique Felix Houphouet-Boigny, Yamoussoukro, Côte d'Ivoire.
Alyssa FegenFaculty of Science, University of British Columbia, Vancouver, BC, Canada.
Ho Yin KamFaculty of Mathematics, University of Waterloo, Waterloo, ON, Canada.
German E NovakovskyDepartment of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
Jasper WongGenome Science and Technology, University of British Columbia, Vancouver, BC, Canada.
Dylan AïssiDepartment of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany.
Li YaoTHU-PKU Joint Center for Life Sciences, Tsinghua University, Beijing, China.

Funding

Faculty of Medicine, University of British Columbia 140
6 · The paper itself

Abstract

backgroundComputational biology requires the reading and comprehension of biological data files. Plain-text formats such as SAM, VCF, GTF, PDB and FASTA, often contain critical information which is obfuscated by the data structure complexity.

resultsbioSyntax ( https://biosyntax.org/ ) is a freely available suite of biological syntax highlighting packages for vim, gedit, Sublime, VSCode, and less. bioSyntax improves the legibility of low-level biological data in the bioinformatics workspace.

conclusionbioSyntax supports computational scientists in parsing and comprehending their data efficiently and thus can accelerate research output.

Indexed as

Computational BiologySoftwareInformation Storage and RetrievalNucleotidesSequence AlignmentNucleotidesCommand line interfaceFASTAFASTQSAMSublimeSyntax highlightingVCFVim

Identifiers

PMID30134911
PMCPMC6106740

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.