Today, the division has created a new online portal for everyone to explore the details of their work and, potentially, human data related to health and disease.

Launched today, the Explorer of the human immune system is the Allen Institute for Immunology’s portal for sharing data with the wider community. Built from anonymized and de-identified data, the site allows scientists to delve into the methods and resources the immunology team uses to analyze and manage their human immunology studies. As the team’s long-term studies of immune health and disease are completed, this data will also be deposited on the public portal. The researchers hope that by making their data available to the public, other members of the scientific community will comb through the data to make their own insights into human immunology that could eventually lead to better and more accurate therapies. for diseases related to the immune system.

When the immunology team established a specialized process, also known as a research pipeline, to conduct multi-year studies of human immune health and disease, including studies of the immune system in COVID-19, cancer and autoimmune diseases, they realized they needed to develop new methods to study the immune system and analyze the resulting data. As they continue to follow healthy and patient volunteers for two years or more, the first public release on the open-access platform contains data and tools related to these newly developed methods. The data from the long-term studies themselves will be published on the public portal in the coming years.

The first public release includes:

  • Protocols outlining the team’s research pipeline, which captures and integrates five different types of molecular data on the human immune system from the same person over time, in addition to clinical data
  • A new method and accompanying data visualization application called TEA-seq, which simultaneously captures three types of data from individual human immune cells: proteins present on the cell surface; all the genes activated or expressed in each cell; and the cell’s “epigenetic” landscape, which gives clues to how its genes are regulated
  • The data and an accompanying interactive visualization of the team’s findings that delay the processing of human blood samples alter certain molecular properties of immune cells (this finding led the team and external collaborators to standardize rapid sample processing of blood after they were collected from the study volunteers)
  • A new method and accompanying data visualization application called PALMO (Platform for Analyzing Longitudinal Multi-Omics data) for analyzing longitudinal multi-omics data, i.e. data that captures multiple types of information, such as genome-wide gene activity or whole-cell protein levels, from thousands or more of individual cells, in samples taken from patients at multiple time points.
  • A set of computational methods, known as Bar itemswhich follows the original source of single cells mixed together in the same experiment, and unmixed them for analysis.

“Since day one at the Allen Institute for Immunology, we’ve always had a plan to openly share our research data, but perhaps more importantly, how we derive that data,” said Tom Bumol, Ph.D., executive vice president and director of the Allen Institute for Immunology. “This first access to the Human Immune System Explorer is really a window into what we are building. Currently, it illustrates some of the techniques and computational environment that we use to solve this important and difficult problem in understanding human immunology.

Cloud Collaboration

The public portal is the latest step in an experimental and computational pipeline that includes a bespoke data analysis and collaboration space for Allen Institute for Immunology researchers and their external clinical collaborators to work together in the cloud. on research projects. This environment, which is also part of Human Immune System Explorer, was created by engineers at the Allen Institute for Immunology in collaboration with Google Cloud.

“Finding insights from complex biomedical research requires powerful tools,” said Joe Miles, General Manager, Healthcare & Life Sciences Industry Solutions for Google Cloud. “The Allen Institute’s Biomedical Platform provides a secure and collaborative environment for scientists with the leading AI platform combined with computing power to answer the world’s most complex health questions and accelerate scientific breakthroughs. which benefits everyone.

This secure platform ensures patient privacy and data integrity, said Paul Meijer, Ph.D., director of software development, database, and pipelines at the Allen Institute for Immunology, and enables researchers to work together seamlessly to prepare data for publication in a scientific journal and for dissemination on the public portal. All patient data is anonymized and anonymized before being uploaded to the closed and secure platform; certain data and other resources will then be made public and accessible on the part of the website.

Meijer and the other engineers on the team had to think carefully not only about patient privacy, but also how to handle such massive amounts of different types of scientific data spanning multiple years in a single study. They want their results to be useful and interpretable for many years to come, which means careful annotation and tracking must be built into the computing environment from the start.

“The Human Immune System Explorer is not just our contribution to open science,” Meijer said. “It is also based on the belief that science is a collaborative activity that involves careful cooperation among a team of multidisciplinary scientists.”

About the Allen Institute of Immunology

The Allen Institute for Immunology is a division of the Allen Institute, an independent 501(c)(3) nonprofit medical research organization, and is dedicated to
understand the dynamic balance of the human immune system in health and disease. The Allen Institute for Immunology will advance our fundamental understanding of the human immune system and identify new therapeutic pathways for disease by employing a multidisciplinary team approach in collaboration with leading research organizations, generating new insights into the drivers cellular and molecular aspects of immune health and diseases related to the immune system.
The Allen Institute for Immunology will launch in 2018 with contributions from founder and philanthropist, the late Paul G. Allen. Data and tools generated by the Allen Institute for Immunology will be publicly available online. For more information, visit

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SOURCE Allen Institute