Automation Software Engineer Jobs (NOW HIRING)

OverviewAbout Excelsior SciencesExcelsior Sciences is reinventing small-molecule discovery and manufacturing through Blocc chemistry-modular, automation-friendly chemistry designed for machines to execute and AI to learn from-combined with closed-loop AI learning systems.Backed by a $70M Series A from Deerfield, Khosla Ventures, and Sofinnova, along with a $25M Empire State Development grant, Excelsior is building a lean, high-leverage organization at the intersection of chemistry, automation, software, and AI. Additional investors include Eli Lilly, Cornucopian Capital, Illinois Ventures, and MIT.Based at the Cure building in New York City, our goal is to build a chemistry and AI-native discovery platform in which high-quality experimental data continuously feeds learning systems that help determine what to make and test next-accelerating the cycle of molecular design, experimentation, and discovery.Overview

This role sits on the Automation team (Physical AI & Lab IT) under the Chief Physical AI Officer, alongside Research Informatics / Software Engineering and Frontier AI (foundation models & AI/Quantum). The Automation team owns the software and systems that connect physical lab devices and robotic platforms to digital lab data and AI agents-enabling reliable, agentic control of automated workflows and closed-loop experimentation.

This role is also the Primary Service Owner for all Lab IT Support at Excelsior Sciences, responsible for lab computer lifecycle, warranty support, setup/configuration, endpoint security, remote access, and lab backup infrastructure.

We are seeking a software engineer with strong experience in laboratory automation and the software that sits at the interface between physical systems and digital/lab-data platforms. You will work as part of a collaborative, cross-functional team alongside scientists, automation engineers, and colleagues from Research Informatics and Frontier AI.

In addition to building automation and orchestration software, you will serve as the primary owner of Lab IT support services-ensuring lab computers; endpoint protection, remote access, and backup systems are reliable and ready for scientific use. The ideal candidate combines solid software engineering skills with practical lab instrumentation knowledge and hands-on Lab IT ownership. Success means automated lab workflows become dependable, observable, and machine-actionable, while the underlying lab computing environment remains secure, supported, and operational.

ResponsibilitiesKey Responsibilities - Automation & Orchestration

• Design, build, and maintain software automation suites and agents that control web and desktop applications driving lab automation devices and integrated workcells.
• Develop software tools that automate manual processes and improve reliability, throughput, and data quality of existing automated workflows.
• Work closely with scientists and automation engineers to design and implement digital solutions and data workflows, with particular focus on instrument integrations and the hand-off between physical execution and lab data systems.
• Build and operate the orchestration and interface layer that allows AI agents (and human operators) to plan, dispatch, monitor, and learn from automated experiments-bridging physical devices and digital/lab-data platforms.
• Conduct testing, troubleshooting, and continuous improvement of automated workflows, including root-cause analysis across software, device, and data layers.
• Contribute to data management strategies and integrations that make instrument and automation data FAIR, high-quality, and usable by both scientists and AI systems.
• Integrate diverse data sources and informatics tools to support holistic analysis and decision-making in early drug discovery.
• Stay current on emerging automation, informatics, orchestration, and agentic AI tools relevant to early drug discovery; evaluate and prototype promising approaches.
• Provide training and support to research staff on automation and informatics tools and best practices.
• Participate in cross-functional meetings to align automation efforts with project and platform goals; uphold high standards of scientific rigor, reliability, and professionalism.

QualificationsKey Responsibilities - Lab IT Support (Primary Service Owner)

• Lab computer warranty support: Own warranty support for all computers within the lab environment, coordinating repairs, replacements, and vendor interactions as needed.
• Lab computer setup: Complete Windows configuration into the Azure environment; install and configure N@W remote access software, SentinelOne endpoint protection, and Datto backup client; install any required equipment vendor software so instruments and workstations are ready for scientific use.
• Lab Backup Server: Own and maintain the Datto server that backs up lab computers; ensure backup integrity, recovery readiness, and ongoing operational health of the lab backup infrastructure.
• Serve as the single point of accountability for Lab IT support needs across Excelsior Sciences, coordinating with the managed services IT team where enterprise network, identity, or broader infrastructure support is required.

Required Skills & Experience

• BS or MS in Computer Science, Software Engineering, Bioengineering, Life Sciences, or a related field.
• 3 to 5 years of experience in digital or laboratory automation, ideally within pharmaceutical, biotech, or high-throughput research environments.
• Proficiency in Python and at least one JavaScript/TypeScript, C#, or R; experience with software development best practices (version control, testing, code review, CI).
• Hands-on experience with software automation and integration approaches (REST APIs, device SDKs, messaging, or equivalent).
• Familiarity with LIMS, ELNs, digital orchestration/scheduling software, and/or cloud platforms (including Azure) used in research settings.
• Practical understanding of laboratory instrumentation and automation technologies; ability to troubleshoot across software and physical systems.
• Hands-on experience with Windows endpoint configuration, Azure AD/Entra join or similar identity integration, endpoint security tools (e.g., SentinelOne or equivalent), remote access solutions, and backup platforms (e.g., Datto or similar).
• Strong communication and collaboration skills; the ability to work effectively with scientists and engineers in a fast-paced environment.
• Ability to manage multiple projects, work independently, and contribute as part of a cross-functional team; comfort serving as primary owner for operational Lab IT support.

Preferred Qualifications

• Experience building or operating agentic AI / multi-agent systems, RAG pipelines, or orchestration layers that interface with physical or lab systems.
• Direct experience with common lab automation platforms (liquid handlers, robotic workcells, integrated schedulers such as Green Button Go, Cellario, Overlord, or similar) and writing control or integration software for them.
• Experience with workflow orchestration tools (e.g., Prefect, Airflow, Temporal, Dagster) or building custom orchestration for lab workflows.
• Familiarity with data pipelines, instrument data models, and making laboratory data machine-actionable for both humans and AI agents.
• Prior work experience in small-molecule, biotherapeutics, or high-throughput discovery environments.
• Comfort operating at the boundary of Physical AI, Lab IT, and digital/AI systems in a startup or platform-building context.

The salary range for this position is $120,000- $175,000 per year. The actual compensation offered will be based on factors such as relevant experience, education, and skills. In addition to base salary, we offer a comprehensive benefits package, including health insurance, paid time off and other benefits.

Excelsior Sciences of New York Is an equal opportunity employer (EEO).  We provide equal employment opportunities (EEO) to all employees and applicants for employment without regard to religion, race, creed, color, sex, sexual orientation, alienage or citizenship status, national origin, age, marital status, pregnancy, disability, veteran or military status, predisposing genetic characteristics or any other characteristic protected by applicable federal, state or local law.

 

 

Location: New York, NY

#LI-DNI

Employment Type: FULL_TIME