Internship Biotech Software Engineer Jobs in Natick, MA

Amide Technologies is a Massachusetts-based biotech company that designs therapeutic peptides and proteins which are difficult to obtain by conventional means, combining solid-phase peptide synthesis with biological expression. By using non-natural amino acids and artificial protein backbones, we design peptides that conventional chemistry and biology cannot reach. Because Amide makes compounds that have never been made before, the work regularly involves problems with no established playbook.

We are seeking a hands-on software engineer to build the automation and scientific software layer that connects Amide’s laboratory execution to its AI/ML platform. This role will focus on data capture, instrument integration, ELN/LIMS connectivity and practical automation for peptide synthesis and assay workflows. You will work closely with lab operations, chemistry, biology, data science and AI/ML colleagues at our Waltham, Massachusetts site.

You will bring recognized expertise in lab automation, scientific software, instrument integration and laboratory data systems. The candidate will lead automation initiatives for peptides and biologics, integrate synthesis workflows and bridge data capture systems to make them ready for modeling. This role is a key part of the platform build because Amide’s AI/ML capability depends on high-quality experimental feedback from synthesis, assays and laboratory operations.

• Design, implement and maintain automation systems for peptide synthesis, biologics workflows, assay execution and laboratory data capture.

• Program, troubleshoot and optimize liquid handlers, robotics, analytical instruments and other lab automation hardware.

• Integrate lab instruments, ELN, LIMS, databases and internal data services so experimental outputs are traceable and model ready.

• Build scientific software tools that cut manual data transfer, standardize how data is captured and shorten the time from experiment to analysis.

• Partner with assay analytics, platform and AI/ML colleagues to support design-build-test-learn cycles.

• Evaluate vendors, automation platforms and outsourced integration support while maintaining clear ownership of laboratory requirements.

• Document workflows, failure modes, operating procedures and data interfaces so the systems can be maintained as the team grows.

• Software Engineer, Lab Automation Engineer, Scientific Software Engineer, or Automation Scientist with a degree in Computer Science, Bioengineering, Engineering, Chemical Engineering or a related disciplin e.

• Strong programming skills in Python, C#, JavaScript or relevant automation software languages.

• Hands-on experience with liquid handlers, robotics, laboratory instruments, scheduling software or other automation systems.

• Experience integrating ELN, LIMS, databases, APIs, instrument files or scientific data platforms.

• Practical troubleshooting ability across hardware, software, data flows and user workflows.

• Experience working in matrixed teams of scientists, engineers and operations colleagues to meet project objectives.

• Strong organizational skills, clear communication and a focus on building reliable systems that scientists can use every day.

• Experience translating laboratory workflows into software requirements, automation methods, data capture steps and acceptance tests.

• Understanding of peptide synthesis, biochemical assays, cell-based assays, analytical chemistry or biologics workflows.

• Experience with vendor selection, external integration partners, outsourced automation support or scientific software contractors.

• Experience with database design, laboratory metadata models, barcode workflows, sample tracking or chain-of-custody practices.

• Familiarity with common lab systems and automation environments such as Benchling, Dotmatics, Thermo Fisher, Beckman Coulter or similar platforms.

• Experience building laboratory systems that directly support closed-loop AI/ML workflows, feeding rapid results from synthesis and assays into datasets that are ready for modeling.

The position is full time and will be based at the company’s headquarters in Waltham, Massachusetts, USA. Flexibility with regard to working hours is required. The Software Engineer, Lab Automation will report to the Chief Data Science Officer.

Amide Technologies offers a challenging and exciting role in one of the Northeast’s most innovative biotech companies. The company offers a competitive compensation package including salary, bonus and equity.

Amide deeply values diversity and is committed to creating an inclusive environment for all employees. We are an equal opportunity employer. We consider all qualified applicants equally for employment. We do not discriminate on the basis of race, color, national origin, ancestry, citizenship status, protected veteran status, religion, physical or mental disability, marital status, sex, sexual orientation, gender identity or expression, age, or any other basis protected by law, ordinance, or regulation.