0. Preface

Shortly after their first full FDA approval, mRNA vaccines have become a hot topic in both science and non-science communities. The technology that enables them has been studied for decades, but it has only recently been used in the real world to stop a global pandemic. mRNA vaccines promise a much shorter vaccine discovery time, easier and scalable production, and much more.

This guide is intended for any computer scientists interested in mRNA vaccine design. It contains an in-depth introduction to mRNA vaccines, from how they work to how they’re designed, representing a quick way to get started in the field (with many optional asides for those interested). I wrote this guide while wearing my programmer hat. It should contain all the biology knowledge required to understand how this kind of vaccine works and how it is developed. The guide starts with the basics (Part 1) and ends up proposing possible antigens for a vaccine against Acinetobacter baumanii infections (Part 2). Lastly, in Part 3, the guide explores how sequences can be subsequently optimized computationally to enhance certain attributes of the resulting vaccine. The steps of the analysis, as well as the logic behind it, should be easy to follow. Anyone could also run the tools used in this guide from the comfort of their own couch, with nothing but a personal computer running Linux.

I should also note this guide, and, more concretely, the pipeline was inspired by my time working with the Instituto de Investigaciones en Microbiología y Parasitología Médica from Universidad de Buenos Aires as a part of an undergraduate civic project with Grupo Insud. This pipeline can be (and has been) applied to other organisms with minor modifications. To publish a (good) paper, however, you’ll likely need to go beyond these steps and validate the results by running lab experiments on mice - that, unfortunately, can’t be done from a couch just yet. My civic project partner, Magnolia Bailey, and I are looking forward to hearing how the antigens we proposed for Klebsiella Pneumoniae performed in tests, as well as to the possible paper that might result from the research.

Lastly, there are three things to keep in mind while reading this guide. First, the whole process of vaccine design is a series of computer science problems ‘hidden’ in biology. The process is powered by major work in fields such as immunology, but using the knowledge of how it all works to design new vaccines is a problem best left to computers to solve. If I can understand the process, so can any computer programmer/software developer out there - hopefully much faster with the help of this guide. Second, I would consider this pipeline new research at the time I’m writing this guide - more people need to apply similar pipelines for so many more targets. That brings me to the last point: mRNA vaccine research is progressing rapidly now that the technology has proven itself. Having more people enter the field means more ideas, leading to faster progress that will benefit many people. Computer scientists are needed. So, without further ado, let’s get going.