Software Engineer, Cheminformatics


Emeryville, CA, US
  • Job Type: Full-Time
  • Function: Engineering Software
  • Post Date: 02/21/2021
  • Website:
  • Company Address: 5980 Horton Street Suite 105, Emeryville, CA, 94608

About Zymergen

We are a science and material innovation company rethinking biology and reimagining the world. A World Economic Forum Tech Pioneer, we partner with nature to create never-before imagined materials and products across industries – from agriculture to electronics, consumer care to pharmaceuticals, and more.

Job Description

We are seeking a software engineer with experience building cloud based data platforms and related web services.  The ideal candidate thrives in a collaborative, fast-paced, multi-disciplinary environment; values clear communication; balances pragmatism and idealism; and is not afraid of ambiguity and incompletely specified requirements. As a team member of the Computational Product Discovery team, there will be opportunities to hone your knowledge in software engineering, distributed systems, scientific computing, and more in the company of experts and expand your skills into a variety of new technologies.  

The Computational Product Discovery team is responsible for building the tools that our scientists use on a daily basis and the computational infrastructure that powers the Zymergen platform. You will apply your Python expertise to large-scale resilient distributed systems, analysis pipelines, and high performance data processing.  Our primary projects in this team involve:

  • Ongoing development of a large-scale chemicals/molecules database, ETL process, and API’s to support a UI and other programmatic interactions.  This has been developed primarily utilizing AWS tools and capabilities.  Integration of that DB and many other chemistry related tools (Electronic Lab Notebook, computational material modeling tools, ML tools, etc), together and interfacing with the existing software infrastructure at Zymergen
  • Development of a data platform to capture and analyze laboratory data from our various chemistry and materials innovation labs. 
  • Supporting infrastructure for machine learning and automated workflows and analysis pipelines for computational material modeling projects developed by the computational chemists on our team.

We are a team that cares deeply about a healthy culture of collaboration, respect, emotional safety, inclusion, exploration, learning and growth.  Our ideal next teammate will be inquisitive and unafraid to ask questions and grow into new domains, they will be a good communicator able to explain complex concepts to people from diverse technical backgrounds, and they will have the emotional intelligence to navigate the inevitable disagreements with respect, humility, and curiosity.

Immediate responsibilities include:

  • Support the development of software to meet the team’s various initiatives as listed above (chemicals and materials databases, data uploaders, support for computational modeling and analysis pipelines, web services for user facing tools, etc.).
  • Evaluating and integrating 3rd-party and open-source tools as needed.
  • Working with a front-end engineer to make sure the overall tooling makes sense, and possibly contributing some front-end code.
  • Learn and grow
  • Help make the world a better place.



  • BS software engineering or related program
  • 3+ years of experience in software engineering. Specifically building cloud based infrastructure for data processing and retrieval
  • Experience developing web services
  • Solid Python experience, or experience with multiple related programming languages.
  • Database development + ORM experience (MySQL, Postgres, Oracle + SQLAlchemy)
  • Penchant for big data and related technologies
  • Mastery of software engineering principles and experience with git, unit and integration testing, and CI/CD pipelines.
  • Excellent written and verbal communication skills.
  • Demonstrated ability to work with a team of highly-motivated engineers


Nice to have: 

  • RESTful API and microservice development
  • Experience with AWS services (Lambda, SNS, SQS, Kinesis, S3 Batch)
  • Docker and kubernetes
  • Infrastructure as code (e.g. Terraform)
  • Elasticsearch
  • Advanced python skills and working knowledge of asynchronous programming, generators, and multithreading techniques
  • Experience with NoSQL technologies, e.g. graph databases is a plus
  • Extra bonus:  Knowledge of chemical toolkits and various structure formats (RDKit, OpenEye, InChI, SMILES, SD File)

Legal authorization to work in the U.S. is required. Zymergen may agree to sponsor an individual for an employment visa now or in the future if there is a shortage of individuals with particular skills for this job.

In compliance with federal law, all persons hired will be required to verify identity and eligibility to work in the United States and to complete the required employment eligibility verification form upon hire.

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Disclaimer: Local Candidates Only
This company does NOT accept candidates from outside recruiting firms. Agency contacts are not welcome.