This spring has been a season of many new learning experiences! Among them, DockerCon 2022 was definitely one that was engaging and inspiring. As the #1 container industry conference for developers that took place online, DockerCon 2022 had an amazing set of sessions that covered a wide variety of topics, ideas, tools, technologies, and real-life examples of how containerization and Docker are being utilized to the fullest.
Before I get carried away with my nerdfest, I should probably share some more details on what containerization and Docker is. Containerization refers to a form of virtualization where applications run in isolated user spaces (called containers) while using the same operating system (OS). That makes each container a fully portable and packaged computing environment. This high level of efficiency is what makes containerization so useful for packaging different microservices in applications. This is the technical explanation, and a more illustrative explanation (and in layman’s terms) is that of containers we see in real life!
They carry shipments of items that are packaged consistently and securely so that nothing gets lost. These containers can transport the items through various forms, i.e. by trains, ships, trailers and trucks. Similarly, containers in the development environment provide standardized packaging and shipping of software. Containers will also work the same way it does on our local machine as it does on our colleagues’ machines. Brilliant!
Now knowing that about containers, Docker is a widely-used open source container platform. It allows developers to package applications into containers — standardized executable components combining application source code with the OS libraries and dependencies required to run that code in any environment.
I often heard about how Docker is very commonly used, especially in the field of DevOps, however, after attending this conference, I now fully understand what makes it stand out. It is not only a tool, but Docker also consists of a whole global community where it has enabled nearly a decade of use (9 years and counting!) and collaborations for numerous projects. The Docker community is a positive and communal environment that is driven by a shared common interest in innovation.
One such example where Docker has brought scientists, analysts, developers, and public health specialists all together was the COVID-19 variant surveillance effort. During this session of DockerCon 2022, Curtis Kapsak (Bioinformatics Scientist at Theiagen Genomics) aptly put it: one of the major barrier to bioinformatics is the vast landscape of computing infrastructure. Enter StaPH-B (State Public Health Bioinformatics)! StaPH-B is a consortium of public health scientists interested in addressing the common barriers impeding bioinformatics implementation in state public health laboratories. They work to achieve this by:
- Providing training and resources for applied bioinformatics
- Supporting construction and maintenance of bioinformatics
- Partnering with CDC and APHL (Association of Public Health Laboratories)
- Taking commonly used bioinformatics tools and use Docker images to make similar builds for public health institutions to use
For SARS-CoV-2 Variant Surveillance, the process consisted of data being generated by taking the collected genetic material from test results of patients. The viral DNA is extracted and then sequenced — from wet lab to dry lab. DNA sequence of the virus variant is then shared publicly for collective research in developing vaccines. Given that there are 2 mutations per month in the 29,903 base genome, there are a lot of DNA sequences to be shared around.
Most of the downloaded Docker images from the StaPH-B library centered on COVID-19 variant surveillance (there have been over a million pulls as of April 2022!). It was pretty incredible to learn about just how versatile Docker is and how it can be used for areas like this in public health. In my previous work experience at the National Institute of Allergy and Infectious Diseases (NIAID, NIH), I had taken the data produced by these bioinformatics to develop programs for COVID-19 diagnostics/treatment research. I now have more insight on the processes that were involved (along with the hard work by many!) in order to produce such valuable information that enabled my line of work on the program management/science diplomacy side.
Overall, DockerCon 2022 has placed containerization on a whole new level for me and I am very excited to continue learning to use Docker in my projects.
Thank you for taking the time to read this, and please follow along more of my experiences!
