08 March 2016 User Stories

Optimizing The Design of New Microbes Using Elasticsearch: An Elastic{ON} Reflection

By Kiyan Ahmadizadeh

At Zymergen, we are combining biology, software, and automation to design new microbes that will revolutionize chemical and material production. To do this, we are creating an industrial biofactory that allows us to build, test, and analyze DNA modifications to microbes at scale. Technology like Elasticsearch has helped us take advantage of the data produced during this process. Thanks to Elasticsearch, our scientists can ask questions of our data that help us explore the vast space of possibilities in DNA.

I attended Elastic{ON}16 as a speaker, sharing our experience at Zymergen using Elasticsearch to help optimize the design of new microbes. The best technical conferences introduce you to new ideas you can apply to tough engineering problems. Elastic{ON}16 was this kind of conference. For example, minutes after arriving on the first day I met Marko Iskander from Adobe, who is using custom scripting with Elasticsearch to improve search results by adding user context to queries. Although font discovery and microbe design are as different as use cases can be, my conversation with Marko and his talk immediately got me thinking about how this technique could be used to improve search results at Zymergen. Learning about Elasticsearch libraries (like the Hadoop, Beats, and Kibana Plugin frameworks) also stimulated exciting new ideas about ETL and analytics. Elastic{ON}16 was rewarding not just for the chance to speak, but also for the chance to learn from fellow engineers developing exciting solutions.

My experience as a speaker was equally rewarding. I was impressed by the support the Elastic team gave as I was preparing my talk for the conference, and their advice was crucial in developing a talk that reached the audience. The lighting, seating, and screen setup at Stage A was energizing and made me feel like an announcer at a sporting event. I appreciated the audience’s attention during my talk, and was delighted by the variety of questions as attendees looked to explore techniques they could apply to their own solutions. Others shared their experiences applying Elasticsearch to problems in bioengineering. This chance to share my experience at Zymergen and learn about the experiences of others was the primary reason I wanted to speak at Elastic{ON}16.

I hope you enjoy this talk on how we’ve integrated Elasticsearch into our software infrastructure. It was a pleasure to share our experiences with such a bright and engaging audience.

zymergen-elasticon-presentation.jpgTo watch the full Zymergen presentation, click the image above or just follow this link

Kiyan Ahmadizadeh builds software that helps organizations in complex industries (like utilities infrastructure or industrial bio-laboratories) make intelligent operational decisions. His work often utilizes cloud computing and NoSQL technologies. His hobbies include running, reading, music, and meditating.