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Extending Galaxy for Large-scale and Integrative Biomedical Analyses

A new Galaxy project sponsored by the Chan Zuckerberg Initiative

We are excited to announce that Galaxy has been awarded a grant from the Chan Zuckerberg Initiative (CZI) as one of the projects in their Essential Open Source Software for Science (EOSS) program. The aims of the CZI EOSS program are to support software maintenance, growth, development, and community engagement for critical tools in biomedical research. We are delighted for Galaxy to join this fantastic program. This project has been awarded to the Oregon Health & Sciences University, Johns Hopkins University, and the University of Melbourne. While these three institutions have been working together to develop features for Galaxy to function better in distributed and cloud computing environments for several years, this CZI grant formalizes this collaboration for the first time, enabling better coordinated efforts.

In this project, we will (1) extend Galaxy to allow easy browsing and importing of datasets from large data repositories; (2) enable Galaxy to efficiently use cloud computing resources for large-scale, near-data computing; and (3) extend Galaxy integration with other data science environments. These new Galaxy features will allow researchers to easily view and fetch data from Google storage and the CZI Human Cell Atlas and bring it into Galaxy, making it straightforward to ingest shared data. New functionality in the Kubernetes-based deployment of Galaxy will enable utilization of remote object data storage directly, skipping the need for a shared file system and improving performance. Lastly, we will enable the Interactive Tools, starting with Jupyter, to operate on the Kubernetes deployment of Galaxy, making this a portable, robust method of deploying ITs for Galaxy anywhere.

We are delighted to commence this project in the coming weeks and welcome input and contributions from the Galaxy community. The software development in this project will help solidify the Kubernetes-based version of Galaxy as a full-featured, robust solution for deploying a production-quality, scalable version of Galaxy on any computing platform, from laptop to computing cluster to a commercial computing cloud.