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bioSyntax: syntax highlighting for computational biology.

Artem Babaian1,2, Anicet Ebou3, Alyssa Fegen4

  • 1Terry Fox Laboratory, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada. ababaian@bccrc.ca.

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|August 24, 2018
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Summary
This summary is machine-generated.

bioSyntax enhances the readability of complex biological data files, aiding computational scientists in efficiently parsing and understanding information. This tool improves data comprehension and accelerates research output in bioinformatics.

Keywords:
Command line interfaceFASTAFASTQSAMSublimeSyntax highlightingVCFVim

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Computational biology relies on interpreting diverse biological data files.
  • Plain-text formats like SAM, VCF, GTF, PDB, and FASTA present challenges due to complex data structures.
  • Key information in biological data files is often obscured by structural complexity.

Purpose of the Study:

  • To improve the legibility of biological data files.
  • To assist computational scientists in parsing and comprehending biological data.
  • To accelerate research output in bioinformatics.

Main Methods:

  • Development of bioSyntax, a suite of syntax highlighting packages.
  • Compatibility with popular text editors: vim, gedit, Sublime, VSCode, and less.
  • Focus on improving the visual representation of low-level biological data.

Main Results:

  • bioSyntax provides enhanced readability for biological data files.
  • The tool improves the user experience in bioinformatics workspaces.
  • Syntax highlighting makes complex data structures more accessible.

Conclusions:

  • bioSyntax supports computational scientists in efficiently parsing and comprehending biological data.
  • The tool can accelerate research output by simplifying data interpretation.
  • bioSyntax is a freely available resource for the bioinformatics community.