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IdeogramJS: Chromosome visualization with JavaScript

Eric Weitz
October 24, 2018

IdeogramJS: Chromosome visualization with JavaScript

The science and software behind Ideogram.js (https://github.com/eweitz/ideogram).

Presented in an hour-long session to an audience of 30-40 software engineers in the Software Engineering Meetup at the Broad Institute in Cambridge, Massachusetts on October 24, 2018.

Eric Weitz

October 24, 2018

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  1. Ideogram.js Chromosome visualization with JavaScript https://github.com/eweitz/ideogram

  2. Outline

  3. What is an ideogram?

  4. Human genome as karyotype

  5. Human genome as ideogram

  6. Parts of a chromosome

  7. p arm q arm Parts of a chromosome

  8. Parts of a chromosome

  9. Ideograms are widely used

  10. Outline

  11. Ideogram.js • • • •

  12. Human genome https://eweitz.github.io/ideogram/human

  13. https://eweitz.github.io/ideogram/mouse Mouse genome

  14. 100+ eukaryotic genomes https://eweitz.github.io/ideogram/eukaryotes

  15. Comparative genomics https://eweitz.github.io/ideogram/homology-interspecies

  16. Show gene location

  17. Load BED files

  18. Diploid human genome

  19. Outline

  20. Ideogram.js software architecture Ideogram.js is a client-side web component. -

    Few dependencies; framework-independent Run-time is JavaScript; data build is Python. Remaining stack: Travis CI, Coveralls, GitHub Pages, Unpkg CDN
  21. Ideogram.js data architecture

  22. ES6 module system

  23. CommonJS, AMD, manual ES6 module system

  24. Ideogram.js modules 2017-07 (v0.6.1)

  25. Ideogram.js modules 2018-08 (v1.3.0)

  26. Ideogram.js modules 2018-10 (master)

  27. Ideogram.js is a reusable component • • • • •

  28. Ideogram.js in React https://github.com/eweitz/ideogram/tree/master/examples/react

  29. Ideogram.js in Jupyter Notebooks https://github.com/eweitz/ideogram/tree/master/examples/jupyter

  30. Outline

  31. Performance Speed matters to users and developers. Users: page load

    time, run-time smoothness Developers: user concerns + time to compile, test, add features
  32. Ideogram.js performance 53 kB in transfer size < 350 ms

    for uncached load and render < 100 ms to filter 20,000+ genes
  33. Measure performance with Chrome DevTools Chrome DevTools panels give key

    insight on web app performance. Network panel: • Detail on each request • Throttle download, upload, latency Performance panel: • Automatic screenshots of visual state over time • “Flame chart” of call stack over time Mac: Command + Option + I Windows / Linux: Control + Shift + I
  34. None
  35. None
  36. Maintainability Performance metrics for developers. Time to: • Compile •

    Test • Add features
  37. Adding new features quickly Code Climate estimates technical debt in

    a repo, by measuring: Argument count Complex logic File length Identical blocks of code Similar blocks of code https://codeclimate.com/github/eweitz/ideogram Method complexity Method count Method length Nested control flow Return statements
  38. Ideogram.js 2019 roadmap • More support for cancer genomics •

    Resurrect batch ideograms • Generalized comparative genomics • Responsive view for mobile