Day in the Life of Software, Whimsy, and Dan

As a part of our “meet the Ginkgo team” series, today we’re featuring a chat with Dan Cahoon, a software engineer (or, software Jedi). Curious how a software engineer ends up working in biology? Read on:

Tell us a little more about your background and what brought you to Ginkgo:

I was a chemistry and biology major in college – but I ended up taking some computer science classes my sophomore year because they counted toward my major. Those ended up being my favorite classes, and I soon figured out I liked coding more than I liked being in the lab, so I went on to minor in computer science. After graduation I was looking for jobs that could combine biology and computer science. Someone in my lab had met one of Ginkgo’s founders (Jason) and connected us, and I’ve been at Ginkgo ever since.

I’ve actually been at Ginkgo longer than anyone besides the founders; they gave me the chance to develop my skills, and believed in me from the start so I could really hit the ground running and apply my biology knowledge to work on some pretty fascinating problems.

What’s your high-level impact at Ginkgo?

It has changed a lot over the years but in short: to make biology easy to engineer, you have to be able to create repeatable engineering experiments. That requires scaling up beyond what you could normally do with just a person working on their own. So I work with our sample tracking system to track what happens in the lab and enable robotic automation and automated data analysis. That process gives our organism engineers superpowers: they can do 1,000 times as many experiments as they would with manual processes.

What’s your typical day like?

I bike into work, and my first task is to sit down in our design studio and code for a few hours. After lunch I’ll have planning meetings or one-on-one check-ins with team members to make sure they’re making progress, have a good idea of what they should be doing and how to do it, and most importantly that they’re happy. We’ll cover things like backlogs and priorities so we can figure out how long various projects will take and commit to getting features rolled out in a timely manner.

Right now my team is creating a link between our sample tracking software and a new automation software, so that we can capture what’s happening on our robotic platforms and not have to manually enter all that information. We’re also building the front end to allow users to specify what their experiments are and then run them on our robotic automation platform.

What’s the most unique part of your day-to-day?

Aside from the software developer side of things, I’m the “Chief Whimsy Officer” at Ginkgo. The role is really about ensuring that we’re having fun while we tackle some really important problems. Creating a culture of whimsy lets people be comfortable coming to work as themselves,  and encourages a happy and safe environment. If people are engaged in their work and feel they can express themselves, they will be better at their jobs and be more productive. It’s just common sense: if somebody is miserable they’ll do the bare minimum. But if you know your day is going to be fun, you’re going to want to show up and do your best work.

I help make sure we’re doing silly things like holding “whimsy office hours” where we can play VR games and make new Slack emoji.  I try to allocate some time out of every week for things like this, because it’s a big part of Ginkgo’s culture to be silly and whimsical. My dream is to run a model train between the foundries to deliver plates of samples around. It’s a system we do need, but I like the idea of bringing in a whimsical touch.

Again, being a software developer at a biology company seems pretty unique. How would you explain your job to other developers?

We’re still serious engineers. Ginkgo is using a lot of cutting-edge developer tools, like React and GraphQL and our developers write Ruby, Javascript and Python. Our software stack has grown tremendously because all our developers are encouraged to evaluate new tech and bring it on board.

At the same time, it’s unique because we’re working on some really powerful science, doing things that have never been done before, and being a part of that is incredible. At Ginkgo, you’re working on something that’s going to change the world, which is more interesting than programming for adtech or changing Google’s search algorithm to be slightly faster. Those things are important, but can’t compare to terraforming Mars with synthetic biology or bringing back the scent of an extinct flower. There’s nowhere else in the world where things like this  are happening on a daily basis, and knowing Ginkgo’s incredible work is propelled by the software I wrote is the greatest part of my job.

Posted By: Grace Chuang

Day in the Life: Chris

In the latest edition of our day-in-the-life series, we hear from Chris Mitchell, Software Engineer about his journey to the engineering team at Ginkgo Bioworks.

How did you become involved in your industry and what led you to work with Ginkgo on the software engineering side?

I actually don’t have a formal education in computer science. I earned my Ph.D. in Biochemistry, Cellular and Molecular Biology from Johns Hopkins and I’ve been a self-taught programmer since the age of 16. Throughout my academic career in the sciences, I spent a lot of time in the lab and became closely acquainted with the huge amount of data and repetitive manual tasks that come with running experiments. For me, software was the perfect way to bridge two worlds I was closely ingrained in to solve some major inefficiencies I was experiencing first hand in the lab. I landed at Ginkgo after someone from the company found my GitHub page and saw some of the tools I was building – new analytical tools for mass spectrometry and sequencing data, as well as a project to enable reproducible data science. After meeting the team at Ginkgo, I was blown away at how quickly they understood the nuances of my work and the caliber of the team. So began my formal entry as a software engineer in the life sciences.

Tell us a little about your role and the impact you have at Ginkgo.

On a fundamental level, Ginkgo could not exist if it weren’t for automation, and automation can’t exist without software. Thanks to the level of automation Ginkgo has brought to the lab, we’ve reached new heights in scale, iteration, data and reproducibility in the synthetic biology industry.

The software engineering team at Ginkgo works with people across a number of different areas, including product management, lab work, analytical pipelines, sales and more. Software is the underlying technology that allows our platform for organism design to operate at such a scale, so it’s essential that we are constantly communicating with every team to ensure things are running smoothly, we’re addressing bottlenecks quickly, and building for the future.

To illustrate how the engineering team’s work affects the larger mission at Ginkgo, I can share a little about one of the projects I’m working on right now. We’re currently working to find a better way for our different users to interact with sequencing data. Sequencing data is used at nearly every stage at Ginkgo: the DNA Fabrication team uses it to verify synthesized sequences, the Build team uses it to verify strain constructs, and the Test team uses it to understand how the transcriptome and other genomic elements contribute to a given phenotype. There are also other indirect users such as data scientists trying to build models to improve future engineering efforts.

Thus, we have a diversity of users – some work with 10,000 samples and some only work with 3-4. It’s really challenging to build a UI and analytical capabilities that capture both ends of the scale in an accurate and consistent way but it is incredibly important. Users need to make informed decisions with as little margin of error. To enable that, we need to build software that permits quick, global insights into their data but also provides the ability to drill down to the most basic elements of a given data type. Users also need to be able to analyze and refine parameters
without rerunning entire workflows that can take hours to complete.

Many people would probably be surprised to hear that you’re a software engineer at a biology company rather than a tech company – what’s that experience been like for you?

A common problem for any software is being built on legacy infrastructure that makes it hard to adapt as technology evolves. Luckily, Ginkgo’s founding team made some smart decisions early on about which stacks we’d build the technology on and we’re continuing to reap the benefits on the developer side. Since then, the leadership and culture at Ginkgo has continued to embrace change and as a developer, I feel empowered to explore and implement new technologies.

For instance, when I came to Ginkgo we were using VMs to run our applications and now we are entirely Docker-based. Similarly, all our UI development is now in React and GraphQL to stitch our data together. These choices have made it so we can standardize the developer experience in terms of spinning up services but still allow some exploration on the underlying tech stack. For example, we have microservices written in Ruby on Rails, Django, Node and Go, which largely were chosen on the basis that the language was the best suited for the particular microservice’s task.

On a more philosophical level, part of the reason why I love working on Ginkgo’s engineering team is that we are building an entirely new frontier. So much of today’s developer role is focused on making something run a half a second faster or increasing ad engagements by 2 percent. Instead, I get to apply those same frameworks and technologies to solve novel problems in synthetic biology, like how to predict the metabolic network for a piece of genetic code.

How have you seen the role of the developer evolve?

The biggest change I’ve seen over the years is a stronger desire from developers and engineers to want to leave a lasting legacy with their work. People in this industry are realizing the power and importance of the technology they work with and want to put those efforts toward bigger problems that can change the world. You’re starting to see developers looking for opportunities where they can have a larger impact and applying their skills to solve big problems in healthcare, sustainability, autonomous vehicles and more.

Posted By: Grace Chuang

Day in the Life of Dawn and NGS

Photo Credit: Grace Chuang

 

 

Today, in our series exploring the day-to-day lives and interests of Ginkgo employees, we talk with Dawn Thompson, Head of Next Generation Sequencing and Senior Biological Engineer at Ginkgo.

 

 

How did you become involved in your industry? Tell us a little bit about your background and the path that brought you to Ginkgo.

I’m a biologist primarily because I love understanding how things work. I’m a geneticist, with the bulk of my training in genomics. The most exciting thing about genomics to me is understanding how the DNA in your genome gets translated into particular characteristics, and how the contents of your genome can be decoded to determine what makes you, you. Of course, people are really complicated, from a DNA perspective, so the simplest way to practice genomics is to look at a simple organism. That’s why I decided to focus on microbial biology. Microbes are fascinating; they live everywhere on the planet — glaciers, volcanoes, even on us — and they do all these fantastic things.

When I was just starting out as a geneticist in graduate school, I was studying one gene at a time, but I knew to really work in genomics I would need to understand entire genomes. I joined the Broad Institute, an arm of MIT and Harvard that was launched in 2004 to improve human health using genomics, and worked there for 9 years studying genomes and their characteristics.

I loved my time at the Broad Institute, but every 10 years or so, I like to look at my career and think: What other cool stuff is there to learn in biology that I haven’t explored yet? To me, synthetic biology was the obvious next step. Synthesizing DNA was getting cheaper, as was sequencing, meaning we could now both “write” (synthesize) and read (sequence) genes in a cheap, high-throughput way. That opened up all kinds of ways to use synthetic biology to understand the functions of cells and program them to serve new functions.

Ginkgo Bioworks was the perfect opportunity to explore synthetic biology and combine my interest in microbes, my expertise in evolution and genomics, and my passion for understanding how things work on a biological level. This August, I’ll be celebrating three years there, leading out next generation sequencing team.

Tell us a little about your role –  what’s the high-level impact you have on Ginkgo?

Ginkgo is divided into two primary departments, foundry teams and customer-facing teams, and as part of my role as a senior biological engineer I’m involved in both sides of the business.

My primary responsibilities are on the foundry side, providing services and support for internal Ginkgo teams and helping our organism engineers determine which of our organism designs are working the best. To do this, my team and I leverage Ginkgo’s next generation sequencing platform (which I played a primary role in creating), allowing the organism engineers to sequence the constructs they use in their organism engineering and sequencing those organisms so that the engineering teams can understand their genomic sequence and ultimately design them.

My team is about 10 people right now, a mix of scientists handling the gene sequencing and bio-mathematicians who can analyze the resulting data.

Photo Credit: Tim Llewellyn

When Ginkgo takes on a new project, we often have a new microbe that we want to work in. My team is one of the first steps in that process. We call it “onboarding a new host organism.” Typically, we can design something on the computer and understand what the sequence will be. But in order to do that, you need to first understand the full genomic sequence of an organism. So for new host organisms we’ll do a custom project where we do several types of sequencing, a lot of computational analysis and then generate what’s called the “reference genome” for them. It’s a really collaborative process.

A real benefit Ginkgo — and our team specifically — offers to our internal engineers is that, because of our next generation mix of automation, we can do all of this in high throughput work cheaply and quickly, speeding up the overall engineering cycle and get answers fast.

Photo Credit: Tim Llewellyn

What’s most exciting to you about the work Ginkgo is doing right now?

Our new agtech company Joyn is super cool. About 15 years ago I was trying to figure out my career, and was fascinated by the idea of going out in the field to sequence organisms in the oceans and soil. Now that’s actually some of the work we’re doing with Joyn as we try to figure out how to engineer a microbe that can live in the soil and help plants grow, replacing nitrogen fertilizer with a more “green” process.

Our tagline is, we’re trying to make biology easier to engineer. In order to do that, we need to understand biology better — and identify the common themes and designs that will help speed up our process.

That will allow us to replace a really labor-intensive, expensive, resource-demanding process with something very green. You can make a lot of stuff both cheaply, and not use a lot of resources that create problems with waste that you need to dispose of. Biomanufacturing is a very cool green process.

Mother nature is the best engineer! If we source all the biodiversity in nature and understand what’s in the genomes in those organisms, it opens up a wide range of functionality. Ginkgo is well on its way to demonstrate that this is a technology that is not only here to stay but can be leveraged to create anything — to make textiles, to replace plastics. If we do it right, we don’t need petroleum based plastics anymore!

Photo Credit: Tim Llewellyn

What do you love most about your job?

It’s hard to pick just one thing, but one of the things I love the most about my work at Ginkgo is that we are using state-of-the art methods to interrogate so many aspects of cellular function. Our sophisticated automation allows us to do this at scale, taking a holistic approach to organism engineering. This is a powerful and versatile way to create organisms for our customers; the resources at Ginkgo allows us to interrogate biology in a way we haven’t be able to previously. We can understand biology on an entirely new level and in turn identify common themes or design principles that can be then be used for a wide variety of applications. It’s almost limitless.

Posted By: Grace Chuang