Helping bioinformaticians transition to running workloads on AWS

By Amazon Web Services

January 9, 2023

This post was contributed by Swaine Chen, Amazon Scholar, APJ Health; Austin Cherian, Sr. Product Manager, HPC; Sarah Geiger, Postdoctoral fellow, National University of Singapore; and Suma Tiruvayipati, Postdoctoral fellow, National University of Singapore

Introduction

Genomics and bioinformatics are transforming all aspects of biomedical research, especially through increases in scale and analysis complexity. Key drivers of these changes are:

  1. Growing data sets from increased output and lowered cost of DNA sequencers and other high-throughput technologies
  2. Improved algorithms enabled by advances in computing, particularly in the cloud
  3. Better and larger online databases being built by research communities
  4. Accelerating expectations in grants and manuscripts for innovating at scale and sophistication

These are exciting times! However, researchers also potentially face challenges with emerging technology, and support from institutions may vary with available resources and expertise. Therefore, while individual breakthrough results from new technology applications might grab headlines, raising the overall research community’s expertise on emerging technologies is also critical and potentially more impactful.

Identifying common challenges

There are numerous resources available to help bioinformaticians learn and work. These span the range from online forums and courses to books and published articles in the scientific literature. Many times, local user groups, the local IT or scientific computing team, or even “asking that person in the other lab” is where support happens. There are also web applications, recipes and code snippets, frameworks and workflow managers, and integrated development environments (or IDE-like solutions like Galaxy or Jupyter notebooks). There are containers and code repositories and online data stores and cloud resources. This rich ecosystem can be daunting for a new user.

We saw a common set of problems among research bioinformaticians, especially with beginning researchers, across four major categories:

  1. Acquiring computing resources. For example, installing a Linux virtual machine on a laptop or getting an account on a university/department cluster. Researchers face many options and technical tradeoffs that beginning users lack context within which to properly decide.
  2. Locating or installing software. Accessing bioinformatics software usually requires some minimal understanding of system administration and package managers or of operating in shared clusters with managed software, such as loading environment modules.
  3. Accessing data. Moving data between different locations often requires basic knowledge of networking, client-server architecture, and authentication. More seamless configurations, such as common shared drives or host-guest integration, may require even deeper knowledge to set up initially.
  4. Analyzing data. Finally, after all this, you can start analyzing data! This is where the diversity of tools and scale of data can generate additional challenges.

Improving the process

With cloud computing, we believe several of these issues can be made easier for a large proportion of budding bioinformaticians. Specifically, cloud computing on AWS provides services that are ideal for completely solving the first challenge of acquiring computing resources. AWS offers virtual servers with Amazon Elastic Compute Cloud (Amazon EC2) and storage with Amazon Simple Storage Service (Amazon S3). Amazon Machine Images (AMIs), the AWS Marketplace, and container registries, such as Amazon Elastic Container Registry (Amazon ECR), can help with the second challenge of getting installed software.  When public data is required (the third challenge above), the Registry of Open Data on AWS can facilitate access to a growing collection of data sets.

The first and second challenges are undifferentiated heavy lifting, and researchers want to quickly move to the third and fourth challenges that are more specific to bioinformatics work. Therefore, to improve the process, we developed a hands-on workshop. The workshop mixes short lectures on new vocabulary, concepts, and considerations with a guided practical tutorial.  The tutorial guides new users to use AWS, provision Amazon EC2 instances, choose from provided AMIs with a curated set of pre-installed software, and move data between their own local laptop or computer and the EC2 instance. The tutorial guides the audience in understanding how to stitch these various steps together to run real world bioinformatics analyses taken from bacterial genomics, long read sequencing, and single cell expression profiling. The tutorial itself is implemented as a website with screenshots and explanations. Users can work at their own pace and refer back to the website in the future. With AWS, you pay for only the services that you use, so running the workshop on one’s own has an estimated total cost of less than $5 USD. If users are eligible, much of it can be done using resources available in the AWS Free Tier.

Attending a workshop

We delivered this “Introduction to Genomics on the Cloud” workshop eight times over the past 18 months. Through online-only events, we reached over 200 participants in 10 countries. The workshops focused on explaining cloud computing concepts and facilitating the hands-on tutorial…

Read the full blog to learn more. Reminder: You can learn a lot from AWS HPC engineers by subscribing to the HPC Tech Short YouTube channel, and following the AWS HPC Blog channel.

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