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BMC Bioinformatics. 2018 Aug 22;19(1):303. doi: 10.1186/s12859-018-2315-y.

bioSyntax: syntax highlighting for computational biology.

Author information

1
Terry Fox Laboratory, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada. ababaian@bccrc.ca.
2
Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. ababaian@bccrc.ca.
3
Departement de Formation et de Recherches Agriculture et Ressources Animales, Institut National Polytechnique Felix Houphouet-Boigny, Yamoussoukro, Côte d'Ivoire.
4
Faculty of Science, University of British Columbia, Vancouver, BC, Canada.
5
Faculty of Mathematics, University of Waterloo, Waterloo, ON, Canada.
6
Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
7
Genome Science and Technology, University of British Columbia, Vancouver, BC, Canada.
8
Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany.
9
THU-PKU Joint Center for Life Sciences, Tsinghua University, Beijing, China.

Abstract

BACKGROUND:

Computational 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.

RESULTS:

bioSyntax ( 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.

CONCLUSION:

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

KEYWORDS:

Command line interface; FASTA; FASTQ; SAM; Sublime; Syntax highlighting; VCF; Vim

PMID:
30134911
PMCID:
PMC6106740
DOI:
10.1186/s12859-018-2315-y
[Indexed for MEDLINE]
Free PMC Article

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