At the annual AWS Life Sciences Executive Symposium, the company announced new Amazon Omics capabilities to help customers build, run, and scale 35 Ready2Run workflows from Element Biosciences, NVIDIA, and Sentieon Inc.
WHY IS IT IMPORTANT
Large scale omics data analysis typically requires specialized bioinformatics workflows to process datasets.
For cases where customers want to run standard analysis workflows without any changes, Amazon Omics now allows healthcare organizations to use Sentieon’s Ready2Run, NVIDIA Parabricks and Element Biosciences, as well as open source pipelines including GATK best practices, nf-core scRNAseq AlphaFold and ESMFold for protein prediction.
AWS announced its blog The new multi-part direct upload API allows customers to upload their data directly to the Omics store and write their output to the sequence store “in minutes”.
According to the announcement, workflows can also be converted to private workflows to support larger files. The transfer manager utility has also been updated to directly download these large files with a single Python command.
In addition to direct data ingestion, other updates include the ability to:
- Leverage NVIDIA T4 and a10 GPUs in Omics workflows to support compute-intensive pipelines and simplify queries and case analysis.
- Automatically parse variant data containing a variant effect predictor annotation into a separate data structure.
- Take advantage of Amazon EventBridge integration and use published events as part of an event-driven architecture.
BIG TREND
In November, AWS launched the Amazon Omics precision medicine cloud platform to eliminate the need for specialized infrastructure and workflows.
The platform uses artificial intelligence, machine learning, and other products and services from AWS and partners to run IT-intensive bioinformatics workflows.
A combination of multiple clinical practices is key to providing care at the Children’s Hospital of Philadelphia, said Jeff Pennington, associate vice president and chief scientist for computer science.
“With Amazon Omics, we can expand our understanding of our patients’ health, down to their DNA,” Pennington said in the launch announcement.
IN RECORDING
“The ease of use, scalability, and transparency of AWS Ready2Run workflows for GATK Best Practices, NVIDIA Parabricks, and Sentieon pipelines greatly reduces barriers to bioinformatics at any scale,” said Dr. Daniel S.T. Hughes, director of bioinformatics at the Institute for Genomic Medicine and the Precision Genomics Laboratory at Columbia University Medical Center, said:
“Combined with native integration into the AWS analytics ecosystem, this should significantly accelerate the pace of clinical genomics.”
Andrea Fox is a senior editor at Healthcare IT News.
Email: afox@himss.org
Healthcare IT News is a publication of HIMSS Media.