About the Solution Engineering Team
Ginkgo’s Solution Engineering team was formed in 2019 as part of the Software Team with the aim of rapidly advancing early stage projects that interface software, biology, and foundries (our biological factories). Ginkgo’s software scrum teams focus on building core applications that are optimized for scalability, availability, and performance. These teams rely on a well-defined Agile process which works well when the domain is well understood. By contrast, the Solution Engineering team operates in a mode that allows for a high tolerance for unknowns and optimizes for development speed to quickly test hypotheses on early stage projects without being locked down to a fixed process.
The Solution Engineering team focuses on solving specific problems quickly by working closely with the Foundry or Codebase teams. Here are examples of projects that we have taken on in the past.
- Designing and implementing the initial version of custom bioinformatics pipelines that allow users of our in-house Next-Generation Sequencing (NGS) services to customize their analytical needs.
- Developing a software- and robotics-driven foundry service that enables process optimization for key raw materials used in the manufacturing of Moderna’s mRNA vaccines.
- Repurposing Ginkgo’s existing NGS lab workflows and informatics software to support whole genome sequencing of SARS-CoV-2.
- Building software applications that enable Ginkgo’s COVID-19 Pooled Surveillance Testing via NGS method (in development). These applications include proprietary software workflows that enable the lab operations for processing samples and a bioinformatics pipeline that processes sequencing data to deliver testing results.
Common themes of these projects include:
- High degree of biology and software cross-domain knowledge required for designing and implementing solutions.
- Ambiguous and uncertain user requirements that require both biology and software context to discern what user actually wants.
- Fast project turnaround.
The projects and problem space that Solution Engineering work with are very challenging as shown in above themes. For example, the user requirements are often ambiguous and quickly changing. The team has to work closely with users to understand their root problems rather than taking user’s requests directly at face value. Often the team has to work with the users to optimize their processes on the biology side first rather than directly writing software that fits their current needs. Despite the challenges, the Solution Engineering team has been successful in executing these projects because of the unique skill sets, capabilities, and drive of the team. The team consists of engineers who have extensive biological knowledge, excellent software engineering skills, and deep understanding of Ginkgo’s software, robotic automation, and synthetic biology. For example, both Chris Mitchell and I have cross domain expertise in biology and software and both of us have worked closely with the biological engineers in the foundry before joining/founding the Solution Engineering team. The team is able to understand a project’s software needs from biological and foundry processes perspectives with ambiguous and uncertain user requirements. The team works hand in hand with Foundry and Codebase teams to design, iterate, and put software solutions into users’ hands quickly. The close relationship with the Foundry and Codebase teams results in quick iteration of software solutions without extensive involvement of product management. The close relationship with the end users also provides feedback about our foundational software directly to software engineers. These learnings have been valuable to help the product and foundational software teams to guide product direction and prioritization. Overall, the team’s impact on Ginkgo’s fast growing Foundry and Codebase projects has been very direct and critical.
My Experience as a Solution Engineer
The Solution Engineering team really excites me because of the interdisciplinary and inter team work we’ve been doing across synthetic biology, lab automation, and software. I’ve always been passionate about driving synthetic biology into a true engineering domain since my PhD study. I learned both the wetlab and software side of synthetic biology during my PhD but found myself most excited about writing software that improves the design-build-test-learn cycle in synthetic biology. I joined Ginkgo in 2017 right after finishing my PhD to pursue the software work, which really aligns with Ginkgo’s mission of making biology easier to engineer. The Solution Engineering team’s approach of working closely with Foundry and Codebase to quickly iterate through software solutions really excites me because I get to learn so much about the state-of-art science and technologies from my colleagues at Foundry and Codebase teams. Over the course of my work, I dig deeply into their problem domains and come up with the best software solutions to help drive their science and technologies forward. For example, I work very closely with our NGS team and work with the most current NGS technologies such as Illumina’s and Oxford Nanopore’s. I learned in detail their workflows for preparing samples for sequencing using a combination of robotics and human tasks and wrote software that orchestrated the workflows for preparing thousands of samples a day for sequencing.
Another aspect of Solution Engineering I think that’s very special is that I get to actually influence the biology and foundry process side. For example, we are building a high-throughput, multi-step Foundry process that spans multiple Foundry teams that requires extensive biological and process controls. I played a crucial role in defining what the layout of these controls should be across many plates in the entire process. Because I write the software that maps the whole process into actual robotic and human operations, I have the most detailed end to end picture. At the end of day, it’s super satisfying to see the software I wrote being used in Ginkgo’s platform to advance our capabilities to engineering biology.
Our team is actively looking for stellar Software Solution Engineers who are interested in working closely at the exciting intersection of biology and software to make biology easier to engineer! Please apply here if you are interested!
(Feature photo by Olav Ahrens Røtne on Unsplash)