Jun 25, 2021

Coding for microbes: A day in the life of a software engineer at Zymergen

As part of our We Make Tomorrow conversation series, Kiyan Ahmadizadeh talks about the software that builds bio-based products — and the value of bringing your whole self to work.

Kiyan at Zymergen, coding for microbes

Kiyan has been leading software projects at Zymergen since 2015, helping to automate the “build” phase of the design-build-test-analyze-learn cycle in biofacturing. Here, he shares some of the ways we use software at Zymergen, and how he hopes biofacturing will positively impact people’s everyday lives.

Can you share a little about your work?

I’m a software engineer, and my team works on the code we use to construct microbes at Zymergen to make useful chemicals and materials. Our software helps with the processes to physically make the yeast or bacteria we use as microscopic factories.

How does software fit into the big picture of ‘making things with biology’?

I’m an engineer, so I tend to think of it in terms of our design-build-test-analyze-learn (DBTAL) cycle. In the design phase, there are software tools that help us understand what chemicals you could potentially make with biology, and also how to design the genes of an organism to actually make that chemical. But then you have to physically make those things in the lab — that’s the build phase, and that’s where my team’s software comes into play. Later in the DBTAL cycle, there are software tools like StrainBrain that analyze what versions of our microscopic factories are performing the best and why, and we use that knowledge to improve on our designs.

What are some examples of how the ‘build’ software works?

For example, our software tracks the physical material involved in making these microorganisms. This means tracking the bits of DNA, as well as the new physical microorganism itself. That sounds simple enough, but we’re talking about making, say, 1000 different organisms at a time, right? So how you define and organize that process is important when it comes to analyzing your results and making the next round of changes to the organism’s designs.

How has your work changed over time?

I’ve been at Zymergen for about five years now, and my projects have changed a bit over time. One of my first projects was called Polaris, which aimed to define the specific operations you need to build microorganisms, and then automate them to build things better and faster. In the early days, Polaris didn’t actually talk to robots. Now, thanks to efforts by the Software Build Team and our Automation Platform Software (APS) Group,, the software that defines how to execute the actual process for making a microorganism can talk directly to the robots who are doing the work. Even compared to just a couple of years ago, we are way farther along that path and way more automated than ever before.

Reconfigurable Automation Carts, or RACs, are automated with software to build microbial factories by the thousands.

What’s your favorite project these days?

Oh, that’s a hard question, because there are so many projects to be excited about. . But a lot of what I’m excited about right now is that many of my projects involve making the tools that enable people to connect different parts of our platform together — which in a sense helps make Zymergen happen. So for example, giving people the underlying tools for connecting design software to robots, or automating build and analysis to improve the DBTAL cycle. The Build team has also been working on multi-edit builds, which is a way for us to try more genetic changes faster. A lot of the software we’re rolling out these days makes everybody run quicker and build things faster. So I’m definitely excited about that.  

As a software engineer at a biofacturing company, how important is it for you to understand biology?

A lot of my work involves coming to understand other people’s work, and then figuring out how our software team can build tools to make that work faster and smoother. And most of the time the work we’re talking about is biology. I’m not a biologist, but I need to pick up that domain knowledge and really connect with people about how the biology works and what’s really in their way. That’s a big part of what we do. It’s also great that the work we’re supporting helps people right where you work, so there are a lot of great opportunities to see the impact you’re having on people’s daily work and to see the whole company move faster. That’s really cool. 

How do you explain what Zymergen does to someone who doesn’t know much about biotech?

I like to say that Zymergen is a company that makes new chemicals or materials using living things. If they are curious to know more, I often use the analog of beermaking, except that instead of using fermentation to make beer, we can use it to make a fragrance, a medicine, or a phone screen. For some, when I talk about using the power of life to manufacture these and other substances in a faster, greener way, it can start to sound a little like science fiction. Sometimes people get kind of scared of that because so many science fiction stories end in disaster. So it’s important to share with people what a positive relationship with nature can look like. I think that reminds people about the benefits for humanity and gives them hope rather than fear. That’s an idea I’m really excited to help communicate: Biofacturing doesn’t have to be this adversarial relationship, and it doesn’t have to be a scary thing.

What impact do you hope to make in people’s everyday lives?

Many of us use a plastic water bottle on a daily basis — it’s made from oil. The same thing with our clothes — you may literally be wearing oil on your back. To me, Zymergen is changing the way we make physical things — changing the underlying paradigm from petrochemistry to biology. One day, we might all be carrying around water bottles and wearing clothes that are made with biology and are better for the environment. Even our phones require parts that are hard to obtain sustainably, but biology can change how we make things in the first place and give us things like bendable screens. There are so many fantastical things we could make, wonderful new things that seem unbelievable or impossible today. To think of the changes we could have on the things we interact with on a daily basis really excites me. 

What makes you most proud to work at Zymergen?

In software engineering, there are lots of jobs out there to build social media tools, target ads at people, create mobile apps, and so on. I’m proud that Zymergen wants to make real things that have a real impact on people, for the better. There are so many ways you can put your expertise out there, but there are very few where you can have such a broad, positive impact on the world. I’m proud to work at Zymergen because not only are we making a real product, but also we care if the impact of that product is good or bad. I’ve worked in other places where that’s just not the mindset, and the difference is night and day. It just makes me immensely proud to work here.

What is it like working at Zymergen?

I was raised in Pennsylvania, my mom’s Puerto Rican, my dad’s from Iran, and I’m a queer person. It’s important for me to honor the diversity that’s a part of me and live as my whole self. Zymergen is a place where I find a lot of support and acceptance, and where I’ve also just been able to be myself without concern. That environment has helped us to attract some of the brightest people, and also allowed me to do my best work. I just really appreciate that.