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Syntax Highlighting for Computational Biology.

Our goal is to make data intuitive for scientists and help you navigate and comprehend its significance. Currently supporting .sam, .vcf, .fasta, .fastq, .gtf, .bed, .pdb, .cwl, & more formats.

Tell us how bioSyntax can develop to help your workflow. (Survey ~5m)

INSTALL bioSyntax

Usage

bioSyntax integrates seamlessly with vim, less, gedit, & sublime to automatically recognize your favorite biological file formats. To gain the most insight from your data, read our brief bioSyntax Manual.

Large data can also be directly piped into less with sam-less, vcf-less, …, xyz-less commands.

Example less command

 

Collaborate

We’re actively developing bioSyntax; we’d love to hear your comments, feedback and suggestions for further development. Drop us a line on github or email.

If you’d like to help out, have intimate understanding of a scientific data-type, or are looking for a fun design / optimization problem check the development page.

Updates

2018-08-22 - bioSyntax publication

2018-08-13 - bioSyntax v1.0 Release

  • Syntax highlighting for FASTA, FASTQ, CWL, BED, GTF, PDB, PML, SAM, VCF file formats
  • Available for: less, vim, gedit, sublime and VScode
  • Updated installer script + packaged documentation
  • Welcome Dylan Aissi + Li Yao on as developers

2018-04-11 - bioSyntax v0.1-beta4 + Development Survey

  • We’re working on a user experience survey to focus development.
  • New Syntax vim-nexus
  • New Syntax vim-pml & sublime-pml(Pymol Script Language)
  • New Syntax cwl-sublime and cwl-vim (Common Workflow Language)
  • Add bam-less alias for sam-less by default
  • Removed sudo requirements for linux-gedit & linux-less installations
  • Alternative Syntax: vim_fasta-ORF: Syntax for finding and highlighting Open Reading Frames

Thanks to

  • Luis Carvalho for vim-nexus
  • @manabuishii for cwl-sublime and cwl-vim
  • @speleo3 for vim-pml & @bbarad for sublime-pml

Past releases