Preparing for Bioinformatics in the Cloud


Wisconsin State Laboratory of Hygiene
Kelsey Florek, PhD, MPH
August 27, 2021

Slides live at:
www.k-florek.net/talks

From an AWS Perspective

... As a Service

... As a Service

How infrastructure as a service works

Virtual Private Cloud (VPC):

An secure, isolated, private virtual network dedicated to your cloud account. Provides isolation between different cloud users where your resources are not shared with other users.

Cloud infrastructure can be used in lots of ways

(you only pay for you what you use)

  • Storage only solution
  • Connect to VPC resources through secure internet tunnels
  • Connect to VPC through a VPN or directly connect VPC to your on-prem network
  • Create permanent instances (virtual computers) that run indefinitely
  • Create/destroy instances on demand (AWS spot)

Utilizing bioinformatics workflows with AWS

The hard part:

Setting up a cloud infrastructure...

Setting it all up yourself

StaPH-B Nextflow AWS Batch Tutorial

AWS Nextflow Quickstart

AWS Nextflow Quickstart

AWS Illumina Dragon Quickstart

AWS Illumina Dragon Quickstart

Moving up the pyramid

Cloud can offer more than infrastructure

  • AWS Lambda: serverless functions (FaaS)
  • AWS RDS: SQL database
  • AWS DynamoDB: non-relational (NoSQL) database
  • AWS SageMaker: machine learning model development environment
  • AWS Redshift: petabyte-scale data warehouse service

Example AWS PaaS use case

WI SARS-CoV-2 Dashboard

Tips for implementing a cloud service

  • Find IT allies
  • Evaluate costing (persistent, on-demand, spot)
  • Take advantage of low-cost options
  • Plan a monitoring approach (billing, budgets, alarms)
  • Consider data backups