Software Engineer III, Computational Structure Determination

About Generate:Biomedicines

Generate:Biomedicines is a new kind of therapeutics company – existing at the intersection of machine learning, biological engineering, and medicine – pioneering Generative Biology™ to create breakthrough medicines where novel therapeutics are computationally generated, instead of being discovered. The company has built a machine learning-powered biomedicines platform with the potential to generate new drugs across a wide range of biologic modalities. This platform represents a potentially fundamental shift in what is possible in the field of biotherapeutic development.  

We pursue this audacious vision because we believe in the unique and revolutionary power of generative biology to radically transform the lives of billions, with an outsized opportunity for patients in need. We are seeking collaborative, relentless problem solvers that share our passion for impact to join us!  

Generate:Biomedicines was founded in 2018 by Flagship Pioneering and has received nearly $700 million in funding, providing the resources to rapidly scale the organization. The Company has offices in Somerville and Andover, Massachusetts with over 300 employees.  

The Role: 

At Generate, we leverage advanced machine learning models to design new drugs in silico. Our approach is complemented by rigorous in vitro characterization of these drug candidates. A key biophysical technique we employ is cryogenic electron microscopy (cryoEM), which enables the direct visualization of a drug candidate’s three-dimensional atomic structure. To support this, Generate has established a state-of-the-art cryoEM facility in Andover, Massachusetts. Our goal is to expand the use of cryoEM as a foundational tool in biotherapeutic discovery through innovative technology and scalable automation. 

We are seeking a software engineer with a strong scientific background to develop and implement a system for automatically determining 3D atomic structures from cryoEM images. This role involves analyzing terabytes of raw image data daily, utilizing an advanced suite of algorithms that includes computer vision, machine learning, and physical simulation. Managing and monitoring these pipelines across numerous weekly data collections necessitates a robust, purpose-built scientific software system. The candidate will collaborate closely with cryoEM experts and cloud architects at Generate to develop this software solution. 

Here's how you will contribute:

• Work with a small team of computational and experimental cryoEM scientists to develop a system that orchestrates, executes, and monitors cloud-based cryoEM data collection and processing pipelines. 

• Maintain and grow this codebase, integrating new cryoEM algorithms and ML-based decision-making tools as they are developed both internally and externally. 

• Aid cryoEM scientists who actively use this system, including training and debugging.  

The Ideal Candidate will have:

• A strong foundation in software engineering with a proven track record of delivering large-scale solutions, especially systems that automate and monitor scientific, ML, or data science workflows. 

• Expertise in a quantitative or physical scientific discipline, such as biophysics, chemistry, physics, computer science, or applied math.  

• Experience following software engineering best-practices including software versioning, integration and unit testing, and CI/CD.  

• The ability to self-manage one’s work, scoping projects with achievable deadlines and communicating clearly with stakeholders.  

• Excellent communication skills with technical collaborators and nontechnical stakeholders, particularly in training and assisting cryoEM scientists to use the system for cryoEM projects.  

• Proficiency with cloud computing (AWS) and network filesystems (FSX).  

• Mastery of the python language. 

• Experience with software packages for 3D reconstruction from cryoEM images and/or atomic modeling software is a plus. 

• Exposure or expertise in electron microscopy, electron microscope automation, or data-informed electron microscope optimization is a plus.

Who Will Love This Job:

Someone who is excited to work on complex challenging problems in a dynamic collaborative environment. Someone who wants to see their work directly contribute to groundbreaking scientific achievements and enable breakthroughs in biotherapeutic discovery.

#LI-HM1

Generate:Biomedicines is 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.

COVID Safety:

Generate:Biomedicines enforces a mandatory vaccination policy for COVID-19. All employees must be fully vaccinated and have received a booster.  The purpose of this policy is to safeguard the health of our employees, their families, and the community at large from infectious disease that may be reduced by vaccinations.  The Company will make exceptions to this policy if required by applicable law and will consider requests for an exemption from this policy due to a medical reason, or because of a sincerely held religious belief, or any other exemptions that may be recognized by applicable.

Recruitment & Staffing Agencies: Generate:Biomedicines does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Generate:Biomedicines or its employees is strictly prohibited unless contacted directly by the Company’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of Generate:Biomedicines and the Company will not owe any referral or other fees with respect thereto.