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Bioinformatics Software Engineer

Location: Option to work on-site in Boston, MA, or remote.


Concerto Biosciences

At Concerto Biosciences, we are obsessed with microbes. We dream of a healthier world where microbial ecology enables advanced medicines and environmentally-conscious agricultural practices, and that starts by finding the right microbes for the job. Using a novel technology from MIT, we screen millions of microbe combinations in parallel to rapidly identify groups of microbes called “ensembles” that perform beneficial functions. This unprecedented scale of screening generates a totally new type of microbiome data, based on direct observation, that lets us map complex microbial interactions. We are currently in the preclinical stage for our first product, an ensemble to treat eczema—a chronic, irritating, and psychologically stressful skin disease that affects over two hundred million people. Our goal is to discover the first-ever treatment that provides totally safe, sustained relief for eczema patients. Concerto will go on to develop a multitude of ensembles that solve the world’s greatest challenges in human health, food production, and bioremediation.

The Concerto team is our most important ensemble. We believe the best human ensembles, much like microbial ensembles, are diverse—composed of individuals with different backgrounds, cultures, genders, and beliefs. We are committed to building a company where you belong and where your voice is heard.


Role Description

The Bioinformatics Software Engineer will be primarily responsible for moving our computational pipeline into production, enabling faster microbial ensemble discovery. As an early engineer on the team, you will have a significant impact on the direction of the data processing infrastructure and you will be encouraged to think critically about how to best handle the novel kinds of microbial interaction data we are generating. You will work closely with the Lead Data Scientist to define the backend data model and lay the foundation for a scalable and quick-turnaround data processing practice at Concerto, enabling a tight feedback loop between engineering and laboratory sides. Your work may touch all aspects of the backend system, from algorithm development and cloud deployment for image processing software through to data storage and API design.

While deep experience in every individual aspect of this system is not required, you should have a working familiarity with standard components of a data processing pipeline and a willingness to jump in and get up to speed quickly. The primary data type you will be handling as an input is image data. NGS data, which we may work with at some point in the future, is not the current focus.

As an early member of Concerto’s expanding team, you’ll also play a critical role in developing Concerto’s culture and translating our core values into practice.


Responsibilities
  • Design and implement an automated, cloud-based pipeline for scalable and repeatable processing of laboratory image data
  • Work with data scientists and laboratory scientists to iterate on data storage and API designs to facilitate analysis of novel data describing microbial behaviors and interactions
  • Manage and optimize cloud deployment of analysis pipelines
  • Integrate monitoring tools and automated tests into deployed workflows to enable efficient debugging
  • Maintain clear documentation for the tools you build
  • Implement unit tests and CI testing as a consistent practice to ensure code correctness
  • Promote code quality and readability through regular code reviews
  • Embody Concerto’s core values in your work

Required Qualifications
  • ≥5 years of experience as a Software Engineer
  • Experience writing well-formatted Python code in a production environment
  • Experience maintaining and deploying a data processing pipeline to cloud services such as AWS
  • Familiarity with database schema design patterns
  • Willingness to learn about the biological context of the data under analysis to inform backend design
  • Clear communication styles and a willingness to collaborate across engineering and laboratory science teams
  • A motivated and self-driven attitude and an ability to work independently

Preferred Qualifications
  • ≥1 year of experience in a fast-paced startup environment
  • Familiarity with infrastructure-as-code tools such as Terraform or CloudFormation
  • Prior experience working on image analysis algorithms

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