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

Mozilla Sprint 2018

  • We are participating in the Mozilla Global Sprint this year! Get involved with developing for bioSyntax!
  • Date: May 10 - May 11 (9:00 am - 5:00 pm PST)
  • On-Site Location: Mozilla Vancouver, #209-163 W Hastings St, Vancouver, BC V6B 1H5, Canada (NOTE: No on-site parking available)
  • Join us for the pre-Sprint Demo Call on Tuesday, May 8, 16:00 UTC to learn more about the project and how you can contribute, or visit the Sprint master post!

CONTACT:

  • Project Lead: Alyssa Fegen (alyssafegen at alumni.ubc.ca); will be on-site during event
  • Slack Channel (NOTE: Invite link expires on May 13; contact dev team for invites subsequently)
  • Discord Server (NOTE: Invite link expires on May 13; contact dev team for invites subsequently)

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