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Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.

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Title: Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.
Authors: Kouřil, David, Manz, Trevor, Clarence, Tereza, Gehlenborg, Nils
Source: Bioinformatics; Feb2026, Vol. 42 Issue 2, p1-5, 5p
Subject Terms: BIOINFORMATICS software, DATA visualization, BIOINFORMATICS, PYTHON programming language, SOFTWARE libraries (Computer programming)
Abstract: Summary Uchimata is a toolkit for visualization of 3D structures of genomes. It consists of two packages: a Javascript library facilitating the rendering of 3D models of genomes, and a Python widget for visualization in Jupyter Notebooks. Main features include an expressive way to specify visual encodings, and filtering of 3D genome structures based on genomic semantics and spatial aspects. Uchimata is designed to be highly integratable with biological tooling available in Python. Availability and implementation Uchimata is released under the MIT License. The Javascript library is available on NPM, while the widget is available as a Python package hosted on PyPI. The source code for both is available publicly on Github (https://github.com/hms-dbmi/uchimata and https://github.com/hms-dbmi/uchimata-py) and Zenodo (https://doi.org/10.5281/zenodo.17831959 and https://doi.org/10.5281/zenodo.17832045). The documentation with examples is hosted at https://hms-dbmi.github.io/uchimata/. [ABSTRACT FROM AUTHOR]
Copyright of Bioinformatics is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.
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  Data: <searchLink fieldCode="AR" term="%22Kouřil%2C+David%22">Kouřil, David</searchLink><br /><searchLink fieldCode="AR" term="%22Manz%2C+Trevor%22">Manz, Trevor</searchLink><br /><searchLink fieldCode="AR" term="%22Clarence%2C+Tereza%22">Clarence, Tereza</searchLink><br /><searchLink fieldCode="AR" term="%22Gehlenborg%2C+Nils%22">Gehlenborg, Nils</searchLink>
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  Data: Bioinformatics; Feb2026, Vol. 42 Issue 2, p1-5, 5p
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  Data: <searchLink fieldCode="DE" term="%22BIOINFORMATICS+software%22">BIOINFORMATICS software</searchLink><br /><searchLink fieldCode="DE" term="%22DATA+visualization%22">DATA visualization</searchLink><br /><searchLink fieldCode="DE" term="%22BIOINFORMATICS%22">BIOINFORMATICS</searchLink><br /><searchLink fieldCode="DE" term="%22PYTHON+programming+language%22">PYTHON programming language</searchLink><br /><searchLink fieldCode="DE" term="%22SOFTWARE+libraries+%28Computer+programming%29%22">SOFTWARE libraries (Computer programming)</searchLink>
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  Label: Abstract
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  Data: Summary Uchimata is a toolkit for visualization of 3D structures of genomes. It consists of two packages: a Javascript library facilitating the rendering of 3D models of genomes, and a Python widget for visualization in Jupyter Notebooks. Main features include an expressive way to specify visual encodings, and filtering of 3D genome structures based on genomic semantics and spatial aspects. Uchimata is designed to be highly integratable with biological tooling available in Python. Availability and implementation Uchimata is released under the MIT License. The Javascript library is available on NPM, while the widget is available as a Python package hosted on PyPI. The source code for both is available publicly on Github (https://github.com/hms-dbmi/uchimata and https://github.com/hms-dbmi/uchimata-py) and Zenodo (https://doi.org/10.5281/zenodo.17831959 and https://doi.org/10.5281/zenodo.17832045). The documentation with examples is hosted at https://hms-dbmi.github.io/uchimata/. [ABSTRACT FROM AUTHOR]
– Name: Abstract
  Label:
  Group: Ab
  Data: <i>Copyright of Bioinformatics is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1093/bioinformatics/btag035
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              Text: Feb2026
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              Y: 2026
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