The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

Abstract: Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible three-dimensional molecular and cellular atlas of the human body, in health and under various disease conditions

hms-dbmi/higlass-website v0.6.36

HiGlass Project Websit

Vitessce: integrative visualization of multimodal and spatially-resolved single-cell data

Multi-omics technologies with single-cell and spatial resolution make it possible to measure thousands of features across millions of cells. However, visual analysis of high-dimensional transcriptomic, proteomic, genome-mapped, and imaging data types simultaneously remains a challenge. Here, we describe Vitessce, an interactive web-based visualization framework for exploration of multimodal and spatially-resolved single-cell data. We demonstrate integrative visualization of millions of data points including cell type annotations, gene expression quantities, spatially-resolved transcripts, and cell segmentations across multiple coordinated views. The open source software is available at http://vitessce.io

common-workflow-language/cwltool: 3.1.20231020140205

<h2>What's Changed</h2> <ul> <li>fix the pickling error for IO objects by @ndonyapour in https://github.com/common-workflow-language/cwltool/pull/1929</li> <li>gh-actions: record version before building container to publish to quay.io by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1931</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/common-workflow-language/cwltool/compare/3.1.20231020113452...3.1.20231020140205</p&gt

common-workflow-language/cwltool: 3.1.20231114134824

<h2>What's Changed</h2> <ul> <li>gh-actions: need newer setuptools to run setuptools_scm by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1932</li> <li>Update ruamel-yaml requirement from <0.18,>=0.16.0 to >=0.16.0,<0.19 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1934</li> <li>software dependencies: allow newer versions of galaxy-tool-util by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1936</li> <li>skip cwl-utils 0.30 by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1941</li> <li>Update black requirement from ~=23.10 to ~=23.11 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1939</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/common-workflow-language/cwltool/compare/3.1.20231020140205...3.1.20231114134824</p&gt

common-workflow-language/cwltool: 3.1.20231020113452

<h2>What's Changed</h2> <ul> <li>temporarily downgrade galaxy-tool-util to workaround issue with newer conda by @mr-c in https://github.com/common-workflow-language /cwltool/pull/1930</li> </ul> <h3>Deps</h3> <ul> <li>Bump mypy from 1.6.0 to 1.6.1 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1927</li> <li>Update black requirement from ~=23.9 to ~=23.10 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1926</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/common-workflow-language/cwltool/compare/3.1.20231016170136...3.1.20231020113452</p&gt

HiGlass: web-based visual exploration and analysis of genome interaction maps

We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, allowing users to combine various data types, synchronize multiple visualization modalities, and share fully customizable views with others. We demonstrate its utility in exploring different experimental conditions, comparing the results of analyses, and creating interactive snapshots to share with collaborators and the broader public. HiGlass is accessible online at http://higlass.io and is also available as a containerized application that can be run on any platform.National Institutes of Health (U.S.) (U01 CA200059)National Institutes of Health (U.S.) (R00 HG007583)National Institutes of Health (U.S.) (U54 HG007963