Software Engineer II, Pipelines and Workflows

Cambridge, MA USA
Jul 19, 2021
Required Education
Position Type
Full time

What if you could join a rapidly growing company and play a critical role in bringing new medicines to patients through looking at and treating disease in a revolutionary way.

Founded by Flagship Pioneering, Cellarity is the first company developing medicines through an understanding of cell behaviors. The company’s broad platform harnesses single-cell technologies and machine learning to digitize and quantify cellular behaviors, unravel the network dynamics that govern those behaviors, and generate medicines that can direct them. Cellarity is using its platform to design medicines targeting the full cellular and molecular complexity of disease, enabling a quantum leap in the success rate and speed of drug discovery, design and development. For additional information, visit

Position Summary:

  • Be a part of a fast-growing team building out the bioinformatics and machine learning workflows to support a groundbreaking platform driving a new approach to drug discovery.
  • Work side by side in a cross functional team of computational biologists and wet lab scientists to define requirements, design and develop automated data processing solutions.
  • Monitor and maintain workflows for quality and consistency.

Key Responsibilities Include:

  • Work with lab scientists, data scientists, and software engineers within Cellarity to define project requirements for bioinformatics and downstream analysis.
  • Design, implement, deploy and maintain production-quality code with unit and integration tests as appropriate.
  • Communicate requirements and coordinate work with teams configuring external systems such as our ELN and LIMS.
  • Write and maintain documentation of design decisions and code.


  • 4+ years experience developing bioinformatics workflows in industry, or in academia with strong code quality standards. (M.S./PhD in Bioinformatics, Computer Science or related field)
  • Experience integrating bioinformatics workflows into computational biology and machine learning analysis.
  • Ability to communicate and work effectively with internal software and data science teams, external IT contractors and members of other functional teams such biology and chemistry.
  • Commitment to building an inclusive team culture that supports and values contributions from all members, regardless of race, gender, background, etc.
  • Curiosity to learn about new areas of science and biotechnology.
    Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.   Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.