E11 Bio - Associate Computational Scientist

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. E11 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. This position is on-site only, in Alameda, CA.

Responsibilities • Operate and improve automated pipelines that process petabyte-scale volumetric microscopy data reliably from acquisition to complete volumes

• Maintain 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

• Collaborate and coordinate with remote senior engineers to provide fast and reliable hands-on support

• Work with wet lab scientists to identify, build and own new tools for the lab, from QC processes and live dashboards to simple analysis tools

• Train lab scientists on our software tools and turn their experience into actionable feedback

• Help maintain and extend our pipeline-wide tracking dashboard to help catch problems early, improve our processes and make data quality visible across the team

• Contribute to our agentic lab automation efforts by taking on projects to set up AI-driven control of lab instruments, with guidance from senior staff

• Engaging in a culture of excellent documentation, preparation of reports, and presenting results internally and externally

Required qualifications • Bachelor's or Master's in computer science, or another science or engineering field with a computational focus, or equivalent experience.

• Solid software development practices: Python, git, testing, documentation.

• Fluent 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.

• Data science fundamentals: numpy, scipy, and working with large datasets.

• Comfort with Linux administration and computer hardware fundamentals, and a willingness to get hands-on with physical equipment.

• Strong interpersonal and communication skills, and a real interest in translating between people with very different expertise.

• Curiosity about the brain and an appetite to learn neuroscience on the job.

Preferred Qualifications • Experience with servers, storage, networking fundamentals or IT infrastructure.

• Experience with large-scale scientific data and ML workflows, especially imaging data.

• Familiarity with HPC, job schedulers, distributed or cloud computing, and containers (Docker/Apptainer).

• Experience working in a wet-lab or applied lab setting, ideally including software integration of lab hardware, such as writing custom control workflows.

• Experience with reproducible workflows and ops: CI, GitOps, infrastructure-as-code, FAIR data principles.

• Neurotech or BCI background.

Who will love this job • You love solving problems alongside scientists and want to be close to frontier-research.

• You love tinkering and getting your hands on lab hardware and have a track record of identifying bottlenecks and driving innovative hands-on solutions.

• You 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.

• You have a strong desire and intrinsic motivation to work collaboratively and inclusively as part of an interdisciplinary team science effort.

• You are committed to the ethos of open science, and want to see your work transparently disseminated.

• You’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.

Outcomes In the first 6 months you will

• Learn our existing data processing workflows and how to operate and troubleshoot common problems

• Own the processing of a new dataset end to end, with problems caught early and minimal manual intervention

• Assist remote engineers with building out our on-prem hardware and network infrastructure

• Gain familiarity with our agentic lab control processes and standards we use to connect AI models to lab hardware

• Build and own at least one new tool for the lab, such as a QC dashboard or analysis process

• Interview key wet lab scientists and microscopists and identify key areas of friction

• Get to know our pipeline tracking dashboard and the metrics it monitors, and assist with its maintenance

In the first 12 months you will

• Acquire a deep understanding of our data processing workflows and contribute multiple improvements that increase reliability, visibility, or throughput

• Keep our on-prem compute, storage and network infrastructure well-documented and highly available

• Deliver 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

• Extend the tracking dashboard with new metrics and alerts that flag issues before they reach downstream processing

We offer • An opportunity to help change the world and work with some of the most talented and collaborative experts across scientific fields.

• An opportunity to gain experience on a field-defining moonshot effort.

• Excellent medical, dental, and vision insurance through a PPO plan; parental leave.

• Generous time off + paid holidays.

• 401K matching up to 6% of base salary

• Ample healthy and energizing food, including daily lunches.

• Stipend for fitness and wellness activities.

E11 Bio, LLC is an Equal Employment Opportunity employer that proudly pursues and hires a diverse workforce. We do not make hiring or employment decisions on the basis of race, color, religion or religious belief, ethnic or national origin, nationality, sex, gender, gender-identity, sexual orientation, disability, age, military or veteran status, or any other basis protected by applicable local, state, or federal laws or prohibited by Company policy. We strive for a healthy and safe workplace and strictly prohibit harassment of any kind.