E11 Bio - Associate Computational Scientist
About The Position
E11 Bio is a non-profit Convergent Research focused research organization in Alameda, California, advancing connectomics toward whole-brain-scale mapping for humans and other mammals. The organization is a collaborative, interdisciplinary team pursuing neuroscience research with the nimbleness of a tight-knit startup. The Associate Computational Scientist will develop, maintain, and optimize workflows and infrastructure for processing large-scale brain-mapping data. The role helps keep petabytes of imaging data moving reliably from microscope acquisition to finished, processed volumes. It combines data-pipeline work with hands-on support for physical computing and network infrastructure, and daily collaboration with biologists and microscopists to identify ways scientific computing can accelerate research. Projects may range from quality control and real-time data analysis to AI-driven lab automation. This position is on-site only in Alameda, California.
Requirements
- Bachelor's or Master's degree in computer science or another computationally focused science or engineering field, or equivalent experience.
- Solid software development practices, including Python, Git, testing, and documentation.
- Fluency with AI-assisted, agentic development as a daily workflow, including directing coding agents and reviewing and testing their output.
- Data science fundamentals, including NumPy, SciPy, and working with large datasets.
- Comfort with Linux administration and computer hardware fundamentals, and willingness to work hands-on with physical equipment.
- Strong interpersonal and communication skills, with interest in translating across people with different areas of expertise.
- Curiosity about the brain and willingness to learn neuroscience on the job.
Nice To Haves
- Experience with servers, storage, networking fundamentals, or IT infrastructure.
- Experience with large-scale scientific data and machine-learning workflows, especially imaging data.
- Familiarity with HPC, job schedulers, distributed or cloud computing, and containers such as Docker or Apptainer.
- Experience in a wet-lab or applied-lab setting, ideally including software integration of lab hardware or custom control workflows.
- Experience with reproducible workflows and operations, including CI, GitOps, infrastructure as code, or FAIR data principles.
- Neurotechnology or brain-computer interface background.
Responsibilities
- Operate and improve automated pipelines that process petabyte-scale volumetric microscopy data from acquisition to complete volumes.
- Maintain on-premises servers, storage, and networking; diagnose and replace failed hardware; coordinate with vendors; and support scaling across on-premises and cloud compute.
- Collaborate and coordinate with remote senior engineers to provide fast, reliable, hands-on support.
- Work with wet-lab scientists to identify, build, and own lab tools, including quality-control processes, live dashboards, and analysis tools.
- Train lab scientists on software tools and translate their experience into actionable feedback.
- Maintain and extend the pipeline-wide tracking dashboard to catch problems early, improve processes, and make data quality visible across the team.
- Contribute to agentic lab automation projects, including setting up AI-driven control of lab instruments with guidance from senior staff.
- Document work, prepare reports, and present results internally and externally.
Benefits
- Medical insurance through a PPO plan
- Dental insurance through a PPO plan
- Vision insurance through a PPO plan
- Parental leave
- Generous time off
- Paid holidays
- 401(k) matching up to 6% of base salary
- Daily lunches and other healthy food
- Stipend for fitness and wellness activities
- Performance-based bonus of up to 20% of base salary
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What This Job Offers
Job Type
Full-time
Career Level
Entry Level
