Accelerating Research Through
Open Science and Biomedical Technology

Our Science Tech team accelerates the pace and reach of scientific research by identifying and democratizing emerging and valuable methods, tools, and datasets and bringing them to a broad and diverse set of scientists, clinicians, and patient communities. Our tools help scientists come to meaningful conclusions quickly to speed up the process of scientific discovery.

Infectious Disease
Chan Zuckerberg ID

Chan Zuckerberg ID (CZ ID) is an open source metagenomics analysis platform for researchers to rapidly identify new and emerging infectious diseases. CZ ID processes sequencing data to provide actionable information on the state of pathogens in a given set of samples. This allows scientists to make data-driven decisions about when to deploy antibiotics, where to prioritize immunization campaigns, how to shape vector-borne disease surveillance and control efforts, and more.

Chan Zuckerberg GEN EPI

Chan Zuckerberg GEN EPI (CZ GEN EPI) is an open source genomic epidemiology analysis platform for public health departments to investigate disease outbreaks and perform pathogen surveillance using genomic data, starting with SARS-CoV-2. CZ GEN EPI helps public health laboratorians, epidemiologists, and public health officers track outbreaks and variants, and gain an overall picture of how pathogens are spreading in their community. These insights help drive public health interventions that can prevent and contain outbreaks more effectively.

Single-Cell Biology
cellxgene

cellxgene is an open source cell-resolution data publishing and exploratory analysis platform. cellxgene empowers scientists to answer questions about the functionality of cells and tissues, and helps scientists publish complex data to enable reuse by cell biologists and computational biologists. Through standardization and integration of published single-cell datasets, we create a database that enables scientists to answer questions about the function of cells in seconds, instead of executing experiments that take years.

Imaging
napari

Built with a global community, napari is a modern, open source visualization and analysis platform for scientific imaging. napari enables researchers with large 3D, time-series, or multi-channel imaging datasets to visualize and analyze their data using the latest methods in machine learning and scientific computing. Recent advances in microscopy and bioimaging technologies have made generating very large datasets much easier, which makes analyzing them much harder.

napari hub

Built by the CZI Imaging Tech team, the napari hub helps researchers find high-quality image analysis methods that solve their unique data analysis needs. The napari hub hosts a growing ecosystem of open source, community-built napari plugins to help researchers find trusted, relevant, high-quality analysis methods that they can use to quantify their data and gain insights into biology.

Visit our GitHub organization to browse projects.

Technology We Support

Beyond building and disseminating technology in collaboration with the science community, CZI Science also works with many community-led projects that we partner with or support through grants to help advance our mission.

Essential Open Source Software for Science

CZI’s Essential Open Source Software for Science program supports software maintenance, growth, development, and community engagement for over a hundred critical open source tools used by scientists globally.

Shasta

Shasta is a DNA sequencer that assembles genomes in a fraction of the time and cost and with comparable accuracy of traditional methods, and is used by scientists to explore the genomic diversity of all species.

TOOLS TO SCALE PATIENT DRIVEN-RESEARCH

We enable and scale patient-driven research by supporting and amplifying the work of rare disease patient organizations by providing them with tools to leverage patient data, scientific knowledge, and researcher and physician connections in order to accelerate research towards new treatments and cures.

BIORXIV & MEDRXIV

Scientists post preprints, or scientific papers published prior to peer review, on servers such as bioRxiv and medRxiv, which dramatically accelerates their ability to access information and build on each others’ work.

protocols.io

Protocols.io is a platform that allows researchers to discover and openly share up-to-date scientific methods.

Work With Us

In addition to collaboration within an engineering project, collaboration across domains is fundamental to the way we work at CZI. Technology is wonderful and can bring about amazing change, but including domain expertise when discussing solutions is imperative.