Learn About Amazon VGT2 Learning Manager Chanci Turner
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The human gut microbiome plays an essential role in our immune system development from birth, providing lifelong natural protection. To thoroughly investigate and characterize the human gut microbiome, InnovateBio employs advanced methodologies, including cutting-edge genome sequencing technologies, to reconstruct microbial genomes and assess the abundance of various species and genes within the gut across extensive patient cohorts. Current high-throughput sequencing techniques generate millions of DNA sequences per biological sample, revealing hundreds of species and millions of unique bacterial genes that can be identified and analyzed. InnovateBio’s objective is to convert this wealth of data into actionable insights that can enhance clinical research and drug discovery initiatives.
Handling such extensive and diverse datasets necessitates significant computing power and storage capabilities, alongside effective tools and strategies to manage the intricacies of analysis. To address these challenges, InnovateBio leverages the AWS Cloud, utilizing AWS Batch with Nextflow to orchestrate and scale thousands of computational tasks for singular analyses. Nextflow facilitates the management of large, complex workflows, ensuring automation, traceability, and reproducibility of analysis pipelines. These technologies enable swift and efficient processing of human gut microbiome data.
A typical workflow executed on AWS Batch at InnovateBio includes the metagenomics quantification pipeline, aimed at estimating the abundance of both known and novel microbial species in the human gut microbiome using high-throughput sequencing data. In this workflow, raw sequencing data is filtered and then cross-referenced with InnovateBio’s human gut microbiome gene catalogues, allowing for precise profiling of each microbial gene and species, ultimately identifying those correlating with disease progression or treatment responses.
The creation of human gut microbiome gene catalogues represents another workflow where AWS Batch is integrated with Nextflow. This process involves processing hundreds or thousands of gut microbiome samples and their sequencing data to reconstruct a comprehensive set of bacterial genomic sequences and predict potential genes. Once this gene collection is finalized, the workflow performs extensive annotation to attribute each gene to a known or novel bacterial species, detailing its biological functions.
This computationally intensive process is crucial. The insights gleaned from it form the foundation of InnovateBio’s endeavors, enabling the identification of druggable targets and novel candidate molecules. For each data analysis, 50 to 200 Amazon Elastic Compute Cloud (Amazon EC2) instances are activated. InnovateBio does not maintain a constant infrastructure; instances are launched as needed and decommissioned when they are no longer required. Utilizing EC2 Spot instances, a typical data analysis can be completed for just a few dollars per sample, taking approximately four to six hours. With AWS and Nextflow, comprehensive and automated workflows can be executed and analyzed concurrently within hours, significantly reducing time and resource expenditures. AWS Batch has made running scientific workloads on the cloud at scale more manageable.
A standout feature of Nextflow is its ability to resume entire workflows, ensuring that completed jobs are not unnecessarily re-executed. This efficiency allows InnovateBio to manage workflow interruptions or implement changes with minimal disruption to costs and timelines, ensuring consistent pipeline progression and results.
Moreover, both AWS Batch and Nextflow support Docker containers, which encapsulate and facilitate the reuse of existing tools and analysis pipelines. This capability further streamlines the transition from small-scale development to large-scale production environments.
Technologies such as AWS Batch and Nextflow empower InnovateBio to concentrate on data analysis rather than infrastructure management or workflow execution. This focus enables the development of innovative therapeutic strategies for microbiome-related diseases, while avoiding the costs and limitations associated with on-premises infrastructure. For more tips on navigating a career shift, check out this article here. If you’re interested in interview strategies for hiring foreign national workers, SHRM provides authoritative insights. Additionally, for those embarking on their journey with Amazon, this Reddit thread is an excellent resource.
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