Empowering bacterial genomics education with HAQM WorkSpaces

Bacterial genome analysis workshops require specialized bioinformatics tools and substantial computational power to process sequencing data. When Siriraj Medical Research Center planned their “Nanopore workshop: bacterial genome bioinformatics series” for more than 60 researchers, they faced a common challenge: how to provide consistent, high-performance computing environments for complex genomic analyses. HAQM Web Services (AWS) offered the solution through HAQM WorkSpaces, transforming how Siriraj Medical Research Center delivers hands-on bacterial genomics training.

You can use HAQM WorkSpaces to provision virtual, cloud-based desktops known as WorkSpaces for your users. These desktops can run Microsoft Windows, HAQM Linux 2, Ubuntu Linux, Rocky Linux, or Red Hat Enterprise Linux. WorkSpaces eliminates the need to procure and deploy hardware or install complex software. You can quickly add or remove users as your needs change. Users can access their virtual desktops from multiple devices or web browsers. With these benefits, users can be productive without having to worry about their desktop.

The challenge

The bacterial genomics training workshops presented by Siriraj Medical Research Center often encounter significant barriers related to computing resources, software installations, and infrastructure accessibility and scalability.

One of the most pressing challenges is the variation in hardware capabilities among participants in the workshop. Many trainees rely on personal laptops with differing operating systems, processor speeds, and memory capacities, creating inconsistencies in performance. These variations often lead to system crashes, slow processing speeds, and an inability to run computationally intensive genomic analyses effectively.

Software installation and configuration presents the major hurdle. Bioinformatics tools such as EPI2ME, which is widely used for bacterial genome assembly and analysis, require specific dependencies and configurations. Ensuring compatibility across different devices frequently results in delays, with workshop instructors spending valuable time troubleshooting individual participant issues rather than focusing on hands-on learning.

Processing bacterial genome data requires powerful computers that most participants don’t have access to. Without the right computing resources, participants can’t complete their analysis tasks effectively. This leads to unfinished work, frustrated learners, and an overall poor workshop experience. Laptop computers often can’t handle the complex calculations needed for analyzing DNA sequences, making it difficult for participants to practice what they’re learning.

Traditional teaching methods also limit how many participants an organization can train. Many organizations lack the necessary infrastructure to accommodate the growing demand of training, especially for a hybrid or remote training session.

Building a cloud-powered learning environment

Oxford Nanopore Centre of Excellence (Thailand), Yip In Tsoi (AWS Partner), and AWS have jointly initiated and organized a workshop aiming to address these critical challenges in bioinformatics education, particularly those related to hardware limitations, software compatibility issues, and computational power constraints. This collaborative workshop used WorkSpaces as a centralized, cloud-based computation environment for all participants, providing a standardized, cloud-based learning environment. WorkSpaces is a fully managed virtual desktop service that provides users with pre-configured computing resources—so that the same configuration is applied to all training environments.

One of the primary benefits of WorkSpaces is the elimination of installation and configuration delays. All the necessary bioinformatics tools for the workshop—including EPI2ME—were pre-installed and optimized for use, and participants were able to begin the hands-on workshop immediately.

The computational capabilities of WorkSpaces played a crucial role in enhancing the workshop experience. With access to cloud-based processing power, participants could execute genome assembly, sequence alignment, and comparative genomics analyses without encountering performance bottlenecks. The consistency in computational resources enabled every participant to complete tasks at the same pace, fostering a more effective learning environment.

Scalability and accessibility were also key advantages of WorkSpaces. Participants were able to sign in to their WorkSpaces from any device, removing geographical and hardware limitations. The flexibility of WorkSpaces allowed the workshop organizers to accommodate all participants without concerns about computing infrastructure availability.

Workshop outcomes

The three-day workshops used WorkSpaces extensively. Participants engaged in various exercises such as sequencing exercises using Oxford Nanopore Technology (ONT), genome assembly using EPI2ME, and comparative genomics including cgMLST analysis and outbreak strain investigations.

The deployment of WorkSpaces resulted in a seamless workshop experience for all participants without technical difficulties. This was a significant improvement compared to previous workshops, where installation and troubleshooting could take up to 3 hours. Computational performance remained consistent across all participants, allowing them to focus on data analysis rather than dealing with system failures or slow processing speed.

Participant feedback highlighted the effectiveness of WorkSpaces in facilitating bioinformatics training. Many reported that the standardized computing environment enhanced their ability to engage with the workshop, because they didn’t need to worry about hardware limitations or software incompatibilities. Instructors also noted a major improvement in the efficiency of training delivery, because they could dedicate more time teaching rather than resolving technical issues.

Looking forward

The successful integration of WorkSpaces with Nanopore workshop demonstrates how cloud technology can transform education. Because the traditional computing barriers had been eliminated, the workshop participants could focus on bacterial genome analysis.

Moving forward, there is potential to expand the use of WorkSpaces in other genomics training programs—particularly for large-scale initiatives—such as:

Enhancing genome analysis capabilities with AWS HealthOmics
Processing and analyzing large datasets with AWS Batch
Automating the genomic analysis workflow with AWS Lambda

These could further improve bioinformatics education by streamlining data analysis pipelines. Organizations are also exploring the integration of WorkSpaces into remote learning models, enabling broader participation from students and researchers worldwide.

To learn more and get started, contact your AWS account team or the AWS Public Sector team.

Additional resources

Contributors

This blog post was co-written by the Oxford Nanopore Centre of Excellence (Thailand), YIP In Tsoi (AWS Partner), and AWS.

AWS Public Sector Blog