Software Engineer, Lab Automation

Amide Technologies•Waltham, MA

4d•Onsite

About The Position

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.

Requirements

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

Nice To Haves

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.

Responsibilities

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.