bioSyntax: syntax highlighting for computational biology

• Published in: BMC bioinformatics Vol. 19; no. 1; p. 303
• Main Authors: Babaian, Artem, Ebou, Anicet, Fegen, Alyssa, Kam, Ho Yin, Novakovsky, German E, Wong, Jasper, Aïssi, Dylan, Yao, Li
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 22.08.2018; BioMed Central; BMC
• Subjects: Archives & records; Bioinformatics; Biology; Collaboration; Command line interface; Computational Biology; Computer applications; Consortia; Data structures; Deoxyribonucleic acid; DNA; Equipment and supplies; Evaluation; Genomes; Genomics; Information management; Information Storage and Retrieval; Keywords; Legibility; Methods; Nucleotides - genetics; SAM; Sequence Alignment; Software; Sublime; Suites (Software); Syntax; Syntax highlighting; VCF; Vim; Command line interface; Sublime; VCF; Vim; FASTA; FASTQ; SAM; Syntax highlighting
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-018-2315-y

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