Senior Software Engineer, Platform (Python)

At Biomatter we design proteins that don't exist in nature. We build the computational technology to do it, and apply it to engineer new enzymes and proteins for manufacturing and therapeutic applications.

You will join our R&D team, working alongside computational protein engineers to develop and maintain our internal protein engineering platform. Day to day, this means building the tools our scientists rely on to run and interpret their work, and the compute infrastructure those tools depend on — from experiment orchestration to deployment and reliability.

You'll own features end-to-end: shaping the problem with the researchers who will use the result, deciding how the system should be architected, building it, shipping it, and keeping it running. You'll also have room to push the platform forward — proposing new approaches, bringing in technologies that fit the problem, and improving how we work rather than only what we ship.

We're looking for a goal-oriented generalist — someone who takes on a wide range of problems, including ones outside their comfort zone, and thrives in a fast-moving environment where much of the work is turning chaos into structure.

Responsibilities

• Work with computational biologists, ML researchers, and data scientists to turn research requirements into reliable engineering systems.
• Integrate AI models and research code into the core platform.
• Automate manual steps across research and engineering workflows.
• Optimize algorithms and AI pipelines for performance and scale.
• Develop and maintain the pipelines that ingest and process biological data.
• Ensure platform reliability through ongoing maintenance, troubleshooting, and user support.
• Raise engineering standards across the platform through system design, code review, testing, and observability.
• Shape the technical direction and long-term evolution of the engineering platform.

Qualifications

• 5+ years of experience in a software development role, with demonstrated ownership
• of complex systems or features.
• Strong proficiency in Python and modern software development practices, including
• git, testing, code review, CI/CD, and deployments.
• Hands-on experience with cloud platforms, preferably GCP, and comfort working
• across the infrastructure stack — provisioning, deployment, monitoring, and security.
• Breadth across the stack — comfort moving between ML code, data pipelines, and
• infrastructure depending on what the work needs, and the independence to take an
• ambiguous requirement through to a production system.

Preferences

• Background working with ML, data science, computational biology, or
• cross-disciplinary technical teams.
• Experience building with LLMs or AI agents — RAG systems, tool-using agents, or AI-assisted development workflows.
• Experience with HPC environments and job scheduling systems.
• Experience with data pipelines, workflow orchestration, or analytics platforms.
• Interest in cross-disciplinary collaboration and in learning the basics of protein engineering and computational biology.

Our offer

• Gross salary for this position is 5000-7500 €/month, depending on experience.
• Office-based work in Vilnius, with flexibility to work from home when you need it.
• Private health insurance.
• A team small enough that your technical opinions change what gets built, and a platform young enough that there's still architecture left to decide.
• You'll be building for users you know by name — the scientists you share an office with — rather than for an abstract backlog.

Hiring process

1. Screening call with our recruiter.

2. Intro / culture call.

3. Technical interview (on-site).

4. Meeting our leadership team (on-site).