bioSyntax: syntax highlighting for computational biology

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.

bioSyntax: syntax highlighting for computational biology

Release time: - Updated: May 11, 2025, 3:58 p.m.

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.

Accepted manuscript

© Li Yao 2019-2025.