Health/Life Sciences

Allen Institute and Google workforce as much as construct platform exploring the immune system

TEA-seq, one of the tools available on the Human Immune System Explorer. Cell types are in different colors, with each dot corresponding to a single cell. Clusters of cells have similar RNA profiles. (Allen Institute Image)

The Allen Institute for Immunology unveiled a new interactive platform on Wednesday to showcase the human immune system, the Human Immune System Explorer.

Built in partnership with Google, the explorer is a central place for researchers and the public to find analysis tools, resources and data. The platform adds to the growing toolkit of similar resources across the Allen Institute, such as the Allen Cell Explorer and the Allen Brain Map.

It’s also the first time the Allen Institute has leveraged Google’s cloud offerings like Vertex AI to build such a platform. Google’s team meets weekly with institute researchers. “They’ve just been deeply committed to working with people in the Allen Institute,” said Paul Meijer, director of software development, database and pipelines at the immunology institute.

As the platform matures, Meijer anticipates it will be broadly used by immunology researchers worldwide, who will add their data to the platform. It will track different cell types, molecules and other aspects of immunity in healthy people and in people with conditions like COVID-19 and cancer. Here are some of the platform’s current features:

  • Protocols describing how to gather molecular and clinical data over time in the same person.
  • A data visualization app called TEA-seq that captures three types of data simultaneously from single immune cells: proteins on the cell surface, RNAs inside the cell, and ‘epigenetic’ information suggesting which genes are active.
  • An interactive data visualization tool showing how delays in sample processing affect immune cells.
  • A way to visualize multiple types of patient data from different time points, called PALMO (platform for analyzing longitudinal multi-omics data).
Paul Meijer, Allen Institute for Immunology director of software development, database and pipelines. (Allen Institute Photo)

The platform ultimately aims to help simplify the cataloging, visualization and analysis of the massive amounts of data being collected in human studies of the immune system. The institute aims to promote open, collaborative and multi-disciplinary science.

Allen Institute researchers, for instance, are involved in a study examining the immune system in patients with long COVID. Scientists are cataloging proteins present on the surface of patient immune cells over the course of the first infection and for weeks afterwards. They recently found sets of proteins associated with long COVID suggesting that some affected people have high levels of inflammation. That data was recently released in a preprint study and will soon be entered into the new platform.

In a tweet, Google cloud CEO Thomas Kurian said he was inspired by his team’s work with the Allen Institute. “The past few years have put a spotlight on the importance of collaborating to diagnose and treat diseases,” he said.

A multidisciplinary team of lab scientists and 10 software developers built the new platform over about three years, said Meijer. “The team science and team development effort has been the real power that we have at the Allen Institute for Immunology,” he said.

The researchers are also committed to increasing the diversity of human subjects represented on the platform. Ultimately users may be able to filter datasets by people’s pre-existing conditions, social conditions, or other factors.

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