{"id":3976730,"url":"https://alion.io/job/convergent-research-e11-bio-associate-computational-scientist","title":"E11 Bio - Associate Computational Scientist","company":{"id":6914,"name":"Convergent Research","domain":"convergentresearch.org","url":"https://alion.io/company/convergentresearch","size_band":"11-50","is_staffing_agency":false,"employer_type":"direct","is_intermediary":false,"listed_via":null,"ats_vendor":"Lever","truth_index":{"grade":"B","score":84,"open_postings":8,"ghost_share":0,"stale_share":0.625,"repost_share":0,"time_to_fill_p50_days":57,"computed_at":"2026-11-09T06:03:00Z"}},"role":"Science & Research","role_family":"Science & Research","seniority":"junior","employment_type":"full_time","work_mode":"on_site","remote_scope":null,"remote_scope_basis":null,"remote_working_hours":null,"hiring_geo_confidence":"structured","locations":["Alameda, United States"],"countries":["US"],"hiring_countries":[],"hiring_countries_total":0,"salary":{"min":100000,"max":165000,"currency":"USD","period":"year","gross":null,"usd_annual":165000},"salary_estimate":null,"experience_years_min":null,"visa_sponsorship":false,"relocation_package":false,"has_equity":false,"technologies":[{"name":"AI Agents","optional":false},{"name":"Claude Code","optional":false},{"name":"Cursor","optional":false},{"name":"Linux","optional":false},{"name":"NumPy","optional":false},{"name":"Python","optional":false},{"name":"SciPy","optional":false},{"name":"Docker","optional":true},{"name":"GitOps","optional":true},{"name":"HPC","optional":true}],"status":"live","first_seen_at":"2026-11-09T15:36:05Z","employer_posted_date":"2026-11-09","last_verified_at":"2026-11-09T18:20:41Z","board_verified":true,"closed_at":null,"days_open":0,"trust":{"level":"ok","repost_count":null,"flags":[],"days_open":0},"description":"E11 Bio is on a mission to advance connectomics towards whole brain scale for humans and other mammals. We are a collaborative and interdisciplinary team of scientists and engineers engaged in a neuroscience moonshot project to develop a radical technology platform for scalable mammalian brain mapping. E11 Bio is a non-profit Convergent Research focused research organization located in Alameda, California, pursuing blue-skies neuroscience research yet operating like a nimble, tight-knit start-up. Read our technology roadmap.\nE11 Bio is seeking a motivated, mission-aligned Associate computational scientist to develop, maintain and optimize the workflows and infrastructure that process our large-scale brain mapping data. You will be responsible for keeping petabytes of imaging data moving reliably from the microscope to finished, processed volumes. That means helping maintain our data pipelines as well as being hands-on with the physical computing and network infrastructure. In addition, you will interact daily with biologists and microscopists on frontier research to identify new areas where scientific computing may accelerate their progress. For this you will build solutions that solve real problems at the bench: from quality control and real-time data analysis to agentic lab automation.\nThis position is on-site only, in Alameda, CA.\nResponsibilities\nOperate and improve automated pipelines that process petabyte-scale volumetric microscopy data reliably from acquisition to complete volumes\n\nMaintain on-prem servers, storage and networking; diagnose and replace failed hardware, assist in coordination with vendors, and support scaling across on-prem and cloud compute\n\nCollaborate and coordinate with remote senior engineers to provide fast and reliable hands-on support\n\nWork with wet lab scientists to identify, build and own new tools for the lab, from QC processes and live dashboards to simple analysis tools\n\nTrain lab scientists on our software tools and turn their experience into actionable feedback\n\nHelp maintain and extend our pipeline-wide tracking dashboard to help catch problems early, improve our processes and make data quality visible across the team\n\nContribute to our agentic lab automation efforts by taking on projects to set up AI-driven control of lab instruments, with guidance from senior staff\n\nEngaging in a culture of excellent documentation, preparation of reports, and presenting results internally and externally\n\nRequired qualifications\nBachelor's or Master's in computer science, or another science or engineering field with a computational focus, or equivalent experience.\n\nSolid software development practices: Python, git, testing, documentation.\n\nFluent with AI-assisted, agentic development (e.g. Claude Code, Cursor etc.) as a daily workflow, including directing coding agents and reviewing and testing their output.\n\nData science fundamentals: numpy, scipy, and working with large datasets.\n\nComfort with Linux administration and computer hardware fundamentals, and a willingness to get hands-on with physical equipment.\n\nStrong interpersonal and communication skills, and a real interest in translating between people with very different expertise.\n\nCuriosity about the brain and an appetite to learn neuroscience on the job.\n\nPreferred Qualifications\nExperience with servers, storage, networking fundamentals or IT infrastructure.\n\nExperience with large-scale scientific data and ML workflows, especially imaging data.\n\nFamiliarity with HPC, job schedulers, distributed or cloud computing, and containers (Docker/Apptainer).\n\nExperience working in a wet-lab or applied lab setting, ideally including software integration of lab hardware, such as writing custom control workflows.\n\nExperience with reproducible workflows and ops: CI, GitOps, infrastructure-as-code, FAIR data principles.\n\nNeurotech or BCI background.\n\nWho will love this job\nYou love solving problems alongside scientists and want to be close to frontier-research.\n\nYou love tinkering and getting your hands on lab hardware and have a track record of identifying bottlenecks and driving innovative hands-on solutions.\n\nYou are passionate about moonshot neuroscience, and want to broadly accelerate science through long-term commitment to a high-impact project with a tight-knit team.\n\nYou have a strong desire and intrinsic motivation to work collaboratively and inclusively as part of an interdisciplinary team science effort.\n\nYou are committed to the ethos of open science, and want to see your work transparently disseminated.\n\nYou’re mission-driven and are seeking an environment where you can take long-term risks on moonshot science, shielded from academic or for-profit incentives.\n\nOutcomes\nIn the first 6 months you will\nLearn our existing data processing workflows and how to operate and troubleshoot common problems\n\nOwn the processing of a new dataset end to end, with problems caught early and minimal manual intervention\n\nAssist remote engineers with building out our on-prem hardware and network infrastructure\n\nGain familiarity with our agentic lab control processes and standards we use to connect AI models to lab hardware\n\nBuild and own at least one new tool for the lab, such as a QC dashboard or analysis process\n\nInterview key wet lab scientists and microscopists and identify key areas of friction\n\nGet to know our pipeline tracking dashboard and the metrics it monitors, and assist with its maintenance\n\nIn the first 12 months you will\nAcquire a deep understanding of our data processing workflows and contribute multiple improvements that increase reliability, visibility, or throughput\n\nKeep our on-prem compute, storage and network infrastructure well-documented and highly available\n\nDeliver lab automation projects alongside senior staff, such as agentic control of microscopes and other lab hardware, that cut manual steps and free up scientists' time at the bench\n\nExtend the tracking dashboard with new metrics and alerts that flag issues before they reach downstream processing\n\nWe offer\nAn opportunity to help change the world and work with some of the most talented and collaborative experts across scientific fields.\n\nAn opportunity to gain experience on a field-defining moonshot effort.\n\nExcellent medical, dental, and vision insurance through a PPO plan; parental leave.\n\nGenerous time off + paid holidays.\n\n401K matching up to 6% of base salary\n\nAmple healthy and energizing food, including daily lunches.\n\nStipend for fitness and wellness activities.","description_format":"text","description_chars":6527,"description_truncated":false,"requirements":{"experience_years_min":null,"management_years_min":null,"team_size_min":null,"manages_managers":false,"education":{"level":"bachelor","optional":false},"security_clearance":false,"languages":[]},"benefits":["401k plan","Parental leave","Vision insurance"],"hiring_locations":[],"hiring_excludes":[],"relocation_offered":false,"industries":["Science & Engineering","Research 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