UBC Faculty Research and Publications

bioSyntax: syntax highlighting for computational biology Babaian, Artem; Ebou, Anicet; Fegen, Alyssa; Kam, Ho Y; Novakovsky, German E; Wong, Jasper; Aïssi, Dylan; Yao, Li


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.

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