{"id":1262214,"url":"https://alion.io/job/output-biosciences-software-engineer-agents","title":"Software Engineer, Agents","company":{"id":3778277,"name":"Output Biosciences","domain":"outputbio.com","url":"https://alion.io/company/output-biosciences","size_band":null,"is_staffing_agency":false,"employer_type":"direct","is_intermediary":false,"listed_via":null,"ats_vendor":"Ashby","truth_index":null},"role":"Backend","role_family":"Backend","seniority":"middle","employment_type":"full_time","work_mode":"on_site","remote_scope":null,"remote_scope_basis":null,"remote_working_hours":null,"hiring_geo_confidence":"structured","locations":["New York, United States","San Francisco, United States"],"countries":["US"],"hiring_countries":[],"hiring_countries_total":0,"salary":{"min":150000,"max":300000,"currency":"USD","period":"year","gross":null,"usd_annual":300000},"salary_estimate":null,"experience_years_min":4,"visa_sponsorship":false,"relocation_package":false,"has_equity":false,"technologies":[{"name":"CI/CD","optional":false},{"name":"LLM","optional":false},{"name":"Model Context Protocol","optional":false},{"name":"Python","optional":false},{"name":"Tool Use","optional":true}],"status":"live","first_seen_at":"2026-07-27T18:26:26Z","employer_posted_date":"2026-07-27","last_verified_at":"2026-10-03T23:33:10Z","board_verified":true,"closed_at":null,"days_open":68,"trust":{"level":"ok","repost_count":null,"flags":[],"days_open":68},"description":"The Role\nOutput has built a biological reasoning model that understands biology at the scale and complexity life actually operates. Our model independently learned the principles of molecular interactions, opening up drug treatments that were previously impossible. We're already generating therapies that traditional approaches cannot reach. The hardest problems in both AI and biology are being solved here, and there is room for you to own one.\nOutput is currently in stealth, operated by a team of repeat founders and biotech veterans with multiple exits in AI x Bio, and backed by top-tier VCs including Y Combinator.\nYou will build the agent infrastructure that turns model capabilities into usable tools and workflows. This role owns the orchestration layer, the inference serving, the internal tooling, and the interfaces that researchers and external systems interact with.\nYou will design and build the agent orchestration system that composes model capabilities into multi-step workflows, handling sequencing, state management, and error recovery\n\nYou will implement agent skills and tools that expose model capabilities to automated and interactive workflows\n\nYou will build inference infrastructure for serving models efficiently, optimizing for latency, throughput, and reliability\n\nYou will design and build APIs and integrations, including MCP-compatible interfaces, that allow external systems and users to interact with Output's models\n\nYou will build internal tools that accelerate the research team's work, from experiment management to evaluation pipelines\n\nYou will establish and maintain software engineering practices across the team: testing, CI/CD, code review, and documentation\n\nAbout You\nYou have a BS in Computer Science or a related field, or equivalent experience\n\nYou have 4+ years of experience building production software systems\n\nYou have experience integrating ML models into products or workflows, including LLM-based systems\n\nYou have strong Python engineering skills with a track record of building maintainable, well-tested production code\n\nYou have experience designing APIs and building systems that other engineers and researchers depend on\n\nYou are comfortable with cloud infrastructure, containerization, and deployment pipelines\n\nYou think in systems: you design for reliability, observability, and graceful failure, not just the happy path\n\nBonus Points\nYou have experience with LLM orchestration frameworks, agent architectures, or tool-use patterns\n\nYou have experience with MCP (Model Context Protocol) or similar model-integration protocols\n\nYou have a background in biology, chemistry, computational biology, or a related natural science\n\nYou have experience building internal tools that accelerate research or data science teams\n\nYou have experience with inference optimization for large models\n\nOur Values\nHeart: We foster a culture of ownership. We are assembling a team of individuals who are passionate and take pride in their contributions.\nExcellence: We have an unwavering commitment to excellence and continuously challenge ourselves to reach the highest standards.\nPracticality: We value practicality and results-oriented thinking. We are committed to making a tangible impact on the lives of patients and the broader community.\nHonesty: We place a high value on honesty and directness. We firmly believe in addressing issues as they arise, in an open and transparent manner.\nFun: We believe that life is too short to not have fun. Our goal is to create a workplace that is fun, engaging, rewarding and fulfilling.\nWhat We Offer\nWe encourage new and different ideas, creativity and contrarian thinking\n\nHealthy feedback focused environment to help you strive - leadership will have high expectations, regularly share constructive feedback, support you and help you grow, and welcome receiving feedback and ideas from you\n\nYou own your day-to-day management. What we care about is that we all hit our milestones\n\nCompetitive salary and equity in a growing, well-funded startup\n\nExcellent medical, dental, and vision coverage","description_format":"text","description_chars":4087,"description_truncated":false,"requirements":{"experience_years_min":4,"management_years_min":null,"team_size_min":null,"manages_managers":false,"education":{"level":"bachelor","optional":false},"security_clearance":false,"languages":[]},"benefits":["Equity"],"hiring_locations":[],"hiring_excludes":[],"relocation_offered":false,"industries":["Biotechnology"],"lifecycle":[{"event":"open","at":"2026-09-25T20:48:50Z"}],"visa":[],"liveness":{"score":10,"band":"cold","label":"Long shot","p_open":1,"p_active":0.366,"p_room":0.28,"age_days":67,"expected_fill_days":19,"reasons":["conf:14","win:tail","crowd:"],"computed_at":"2026-10-03T05:45:00Z"},"pay":{"stated_usd_annual":300000,"is_top_pay":true},"html_url":"https://alion.io/job/output-biosciences-software-engineer-agents","json_url":"https://alion.io/job/output-biosciences-software-engineer-agents.json","meta":{"generated_at":"2026-10-04T00:56:12Z","cache_seconds":300,"methodology":"https://alion.io/methodology","terms":"https://alion.io/terms","contact":"https://alion.io/contact","api":"https://alion.io/developers","usage":{"tier":"crawler","counted_by":"address","units_charged":1,"used_today":1186,"day_limit":5000,"remaining_today":3814,"minute_limit":60,"resets_at":"2026-10-05T00:00:00Z"}}}