skelviper / chromoskein

Chromoskein

Chromoskein is a tool for visualizing genomic data with a special focus 3D chromatin structures predicted from Hi-C.

The project uses WebGPU which is currently under development. In order to run Chromoskein, you will need experimental versions of modern browsers. We recommend Google Chrome Canary.

Development

Chromoskein is developed at VisitLab from Masaryk University, Brno, Czech Republic.

Project initialization

Windows 10 (Creator's update and later):

• Enable 'Developer mode'

• Clone with symlinks enabled

  git clone -c core.symlinks=true

Run dev server

• cd app
• npm run serve

Browser setup:

• Google Chrome Canary
  • Enable Unsafe WebGPU flag: chrome://flags/#enable-unsafe-webgpu
  • Make sure hardware acceleration is enabled: chrome://settings/system > Use hardware acceleration when available
    • Graphics status can be checked in: chrome://gpu
  • Chromoskein on macOS refreshes when data is loaded in 3D viewport? Disable Back-forward cache flag: chrome://flags/#back-forward-cache. This is probably a bug in Chrome and the flag won't be needed in the future.

Demo

Exemplary deployed version of ChromoSkein is available at https://visitlab.pages.fi.muni.cz/chromatin/chromoskein/

A demo workspace with sample dataset can be found under Workspace > Open exemplary workspace