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

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.

Item Metadata

Title
bioSyntax: syntax highlighting for computational biology
Creator
Babaian, Artem; Ebou, Anicet; Fegen, Alyssa; Kam, Ho Y; Novakovsky, German E; Wong, Jasper; Aïssi, Dylan; Yao, Li
Publisher
BioMed Central
Date Issued
2018-08-22
Description
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.
Subject
Syntax highlighting; Vim; Sublime; Command line interface; SAM; VCF; FASTA; FASTQ
Genre
Article
Type
Text
Language
eng
Date Available
2018-08-22
Provider
Vancouver : University of British Columbia Library
Rights
Attribution 4.0 International (CC BY 4.0)
DOI
10.14288/1.0371198
URI
http://hdl.handle.net/2429/66898
Affiliation
Medicine, Faculty of; Science, Faculty of; Other UBC; Non UBC; Medical Genetics, Department of
Citation
BMC Bioinformatics. 2018 Aug 22;19(1):303
Publisher DOI
10.1186/s12859-018-2315-y
Peer Review Status
Reviewed
Scholarly Level
Faculty
Copyright Holder
The Author(s).
Rights URI
http://creativecommons.org/licenses/by/4.0/
Aggregated Source Repository
DSpace

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Rights

Attribution 4.0 International (CC BY 4.0)