Research Software Engineer

Cambridge, MA, United States

Company Summary:

Each day, the lives of more than 2 billion people across the globe are impacted by chronic diseases. Moreover, the economic burden on society of treating chronic disease is spinning out of control. Today, this dire situation appears unlikely to change as >95% of global healthcare costs are spent on treating rather than preventing chronic diseases. FL84, Inc. is a privately held early-stage company that is applying advanced biological and computational platforms to discover breakthroughs in detection of and intervention against the etiologies that drive progression from health to disease. Our goal is to leverage our proprietary platforms to disrupt the current approach of treating chronic disease too late. We endeavor to provide true health care rather than sick care to individuals that are at risk of progressing to disease.

About Flagship

Flagship Pioneering is a biotechnology company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com. Position Summary:

We are seeking a Research Software Engineer who is enthusiastic about developing, testing and deploying research software that models complex biological systems and their relationship to clinical state changes. The candidate will work closely with computational biologists to deploy prototype methods at scale, develop production-grade workflows for model versioning and testing, package methods into modular application programming interfaces (APIs), and provide overall support for the team’s developer operations (DevOps). An ideal candidate will pride themselves on their ability to build scalable, automated frameworks that are easy to use and maintain. The position will provide a unique opportunity to play a foundational role in the development of FL84’s preclinical platform and treat diseases before they become a burden to the patient or the healthcare system.

Key Responsibilities:

Work closely with the computational biology team to deploy method prototypes in production.

Establish machine learning operations (MLops) workflows that systematically version, train, evaluate and deploy machine learning models.

Design a suite of automated tests and quality control (QC) modules and implement continuous integration / continuous deployment (CI/CD) workflows that make use of them.

Package the team’s methods into modular application programming interfaces (APIs)

Implement automated API documentation generation to increase the overall familiarity and reuse of existing in-house code among the team.

Maintain existing visual dashboard and pipelines.

Optimize existing DevOps workflows to maximize team efficiency and reduce unnecessary compute costs.

Cultivate a data-centric company philosophy by helping to maintain best practices for software development, data management, and infrastructure.

Monitor and evaluate new and emerging technologies that benefit the development of computational biology software.

Basic Requirements:

BS or MSc in computer science, bioinformatics, or related discipline

Extensive Python programming experience, including performance tuning and debugging, software packaging and deployment.

Proficiency with R and Nextflow

Proficiency with git, Docker and AWS

Experience with CI/CD or automated MLops workflows

Excellent communication skills. Must be able to speak and ideate with multi-disciplinary team including biologists. Must be able to think independently, work collaboratively and contribute to an active intellectual environment.

Preferred Requirements:

Strong understanding of biology.

Experience with processing molecular datasets, including single-cell RNA sequencing.

Familiarity with machine learning methods, parameter tuning and performance evaluation.

Experience with data security and authentication workflows.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

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.