Throw your genomic data into space!
uchimata is still in development.
- Genomics semantics: Molecular visualization tools are often used for examining chromatin 3D data. The limiting factor in that case are the missing proper semantics when analyzing the spatial structures. For example, selecting part of the model should be possible using genomic coordinates (not "atom" indices).
- Made for computational notebooks: We need to meet computational biologists where they typically work. Integration in computational notebooks is therefore a critical feature. As a Javascript library, integration in Observable Notebooks is free. Using
uchimatain Python-based notebooks (e.g., Jupyter Notebook/Lab or Google Colab) is made possible thanks to the wonderful anywidget library: see uchimata-py. - Staying small and focused: The many bioinformatics file formats can lead to bloated software that tries to capture every use case. Such software is then hard to maintain. The idea here is to keep
uchimatasmall, doing one thing, hopefully extremely well: visualize 3D chromatin structures with a variety of declaratively specified representations. Additional functionality should be build on top as further libraries and applications. With the computational notebooks integration, we can also afford to leave much of processing to the ecosystem of other bioinformatics tooling.
API documentation is available in docs-api/. The documentation is automatically generated from JSDoc comments in the source code using TypeDoc.
To regenerate the documentation after making changes to JSDoc comments:
pnpm run docsLed by David Kouřil @ HIDIVE lab (Harvard Medical School).
The name uchimata roughly abbreviates "understanding chromatin in models approximating three-dimensional architecture". The tool was previously known as chromospace.