Protein Core Director Jobs (NOW HIRING)

The Institute for Protein Innovation (IPI)is a nonprofit research organization advancing protein science to accelerate research and improve human health. Founded in 2017 and located in Boston’s Longwood Medical Area, the Institute’s three-pronged strategy is to build protein tools, conduct related internal research and develop educational programs for the protein science and biological research communities.

With a significant endowment, IPI uniquely combines the freedom of academia with the high throughput and scale of industry to take on transformative projects. IPI has built a robust platform for discovering, developing, and distributing synthetic antibodies and other protein tools to share with the biomedical community. The Institute's deep protein expertise, collaborative spirit and research tools are powering new biomedical and therapeutic discoveries with a growing community of researchers at Harvard Medical School, Boston Children's Hospital and other institutions across Greater Boston and beyond.

The Institute for Protein Innovation is seeking a Senior Software Engineer to join our Lab Informatics team and help architect, build, and evolve the Institute’s digital laboratory platform, with Benchling as a core component.

This role will partner closely with scientists, automation engineers, and data teams to translate complex scientific workflows into intuitive, scalable, and reliable digital solutions. The Senior Software Engineer will contribute to Benchling configuration and development, scientific data modeling, application and integration development, laboratory automation, analytics, and platform architecture.

This position will play a key role in ensuring that scientific data is structured, traceable, accessible, and reusable across the Institute while establishing strong software engineering practices for our laboratory informatics ecosystem.

Director of Automation and Process Optimization

• Partner with scientists and cross-functional teams to understand experimental workflows, gather requirements, and translate scientific needs into effective technical solutions.
• Design, develop, and maintain the Institute’s Benchling environment, including schemas, Registry entities, Results, Inventory, workflows, notebook templates, applications, and other platform capabilities.
• Develop production-quality applications and integrations using the Benchling Developer Platform, including APIs, SDKs, Apps, App Canvas, events/webhooks, and related technologies.
• Design and maintain scalable scientific data models that support data integrity, traceability, interoperability, and long-term reuse.
• Build scientific analytics, dashboards, and data applications using Benchling Insights, SQL, Python, and appropriate visualization and application frameworks.
• Integrate Benchling with laboratory instruments, automation platforms, internal applications, data systems, and external scientific software.
• Design and implement workflows that enable reliable transfer of experimental data between laboratory automation systems and Benchling.
• Establish and follow software engineering best practices, including source control, code review, automated testing, CI/CD, documentation, deployment, monitoring, and maintainable software architecture.
• Ensure consistent implementation of data standards and maintain high levels of data quality and integrity across the laboratory informatics platform.
• Serve as a technical subject matter expert for Benchling, advising scientists and technical teams on platform architecture, data modeling, integrations, and development best practices.
• Troubleshoot complex platform, application, and integration issues; identify root causes and implement durable, scalable solutions.
• Contribute to the technical roadmap for laboratory informatics and evaluate new technologies and approaches that improve scientific productivity and data accessibility.
• Develop technical documentation, user guidance, and training materials to support adoption of laboratory informatics tools.
• Provide technical leadership through architecture discussions, code reviews, development standards, and mentorship of engineers and technical colleagues.

• Bachelor's degree in Computer Science, Bioinformatics, Software Engineering, Computational Biology, or a related field, or equivalent practical experience.
• 5+ years of professional software engineering, scientific informatics, or related industry experience.
• Hands‑on experience developing on the Benchling platform, including Benchling Apps, App Canvas, APIs/SDK, Events, Insights, and/or Data Warehouse.
• Strong Python and SQL development skills.
• Experience developing production‑quality applications, APIs, and system integrations.
• Experience with REST APIs, webhooks/event‑driven architectures, authentication/authorization, and structured data models.
• Experience with Git, automated testing, code review, CI/CD, and modern software engineering practices.
• Working knowledge of life‑science R&D workflows and scientific data.
• Demonstrated ability to translate complex scientific workflows into scalable software solutions and data models.
• Excellent communication skills and ability to collaborate directly with scientists and technical stakeholders.

• Experience configuring Benchling Registry, Inventory, Results, schemas, workflows, and notebook templates.
• Experience integrating laboratory instruments or automation systems with informatics platforms.
• Experience building scientific dashboards or analytics applications with Plotly/Dash, Streamlit, Tableau, Spotfire, or similar tools.
• Experience in biologics, antibody discovery, protein science, molecular biology, cell engineering, or related life‑science R&D.
• Experience with cloud infrastructure and containerized application development.

$130,000 - $160,000 a year

Compensation commensurate with experience.

• 100% employer-paid medical, dental, and vision plans
• Flexible spending accountsand a healthcare reimbursement account
• 401(k) plan with generous 6% employer match – immediately 100% vested
• Generous PTO package
• Commuter and parking reimbursement
• Career development opportunities

For more information, visit proteininnovation.org or follow us on social media, @ipiproteins. IPI is an independent 501(c)(3) nonprofit research organization and an equal‑opportunity employer. The Institute celebrates diversity and is committed to creating an inclusive environment for all employees. Please be advised that you will be required to provide evidence of your identity and eligibility for employment in the United States. IPI will not guarantee sponsorship of foreign nationals and retains complete discretion regarding providing sponsorship to any prospective or existing employee at time of hire or at any time in the future.