Principal Software Engineer

Bexorg•New Haven, CT

11d•$200,000 - $260,000•Onsite

About The Position

Bexorg is seeking a hands-on Principal Software Engineer to own the software scientists use to design experiments on living human brain tissue and analyze the resulting data. The role leads two key efforts: the company’s custom LIMS, including Cortex for BrainEx and NeuroscaleOps for NeuroScale, and Neurolens, an AI research harness to be re-architected as a multi-tenant platform for large pharmaceutical partners. Reporting to the CTO, the engineer will set technical direction, contribute substantial code, and work closely with scientists and engineers who use the systems in the lab. The engineer will deepen their understanding of BrainEx and NeuroScale experiments and translate that knowledge into structured, validated, and versioned ontologies, schemas, user experiences, and experiment records. The goal is to make experiment design precise and usable while preserving the context and interpretability of historical data. For Neurolens, the role will lead the transition from a single-organization system to a secure, licensing-aware AWS platform for partners. This includes tenant isolation, partner identity federation, governed skills and tools, reproducible provenance, scalable and cost-attributed bioinformatics compute, and observability and evaluation of AI runs. The position also owns production operations, cloud and data engineering, security and compliance practices, technical standards, mentoring, and communication with internal and external stakeholders. Bexorg is a precision neurology company developing CNS therapeutics using its BrainEx platform, which perfuses fresh whole human postmortem brains, and NeuroScale, which supports high-throughput brain-slice experiments. The position is on-site in New Haven, Connecticut, with location flexibility open for a truly exceptional candidate. Compensation is $200,000–$260,000 per year plus bonus; the company also mentions meaningful equity and benefits.

Requirements

Typically 10 or more years of hands-on experience designing, building, and operating production software, including several years as a technical lead or architect for systems used daily by demanding users.
Demonstrated end-to-end product ownership, from user discovery and data modeling through UX, implementation, deployment, operation, and iteration.
Strong expertise in most of the following: modern full-stack web development such as React and TypeScript; API design; and backend services in Python or a comparable language.
Experience with complex scientific or operational data modeling, relational design such as PostgreSQL, schema evolution and migrations, and versioned or bitemporal records.
Experience with formal schemas and ontologies such as JSON Schema, Pydantic, LinkML, OWL/SHACL, or equivalents, and validating data at system boundaries.
Production experience with LLM-powered systems, including tool use and agents, structured outputs, bounded action spaces, evaluation harnesses, and understanding model failure modes.
Deep AWS expertise, including multi-account Organizations, IAM, VPC networking, KMS, S3-based datalakes, container and serverless compute, and infrastructure as code.
Experience with fine-grained, policy-based authorization and entitlements at row, column, and object level, such as AWS Lake Formation, Cedar, or OPA, that accurately reflect contractual terms.
Experience with provenance, auditability, and data integrity, including immutable logs, deterministic re-execution, and controls aligned with standards such as 21 CFR Part 11, GxP, HIPAA, or SOC 2.
Genuine interest in drug discovery and patience to learn experiment design in depth from scientists.
Strong product sense, including the ability to identify usability problems and distinguish requested features from users’ underlying needs.
Fluency in using LLM-assisted engineering in daily work, together with sound judgment about when model outputs are wrong.
Excellent written and verbal communication, with demonstrated experience mentoring engineers and setting technical standards.
Ability to take ownership, move quickly, and drive projects forward with minimal supervision.
Bachelor’s degree in Computer Science, Software Engineering, Applied Mathematics, or a related field, or equivalent industry experience with a strong record of impact.
Based in or willing to relocate to the New Haven, Connecticut area for an on-site role.

Nice To Haves

Experience building or operating large multimodal omics datalakes, including transcriptomics, proteomics, metabolomics, or high-content imaging, and related bioinformatics tooling such as Nextflow, Snakemake, scanpy, or Seurat.
Experience with LIMS, ELN, or sample-tracking systems, whether commercial or custom-built.
Life-sciences ontology engineering, including OBO Foundry ontologies, knowledge graphs, or semantic-web tooling.
Multi-tenant SaaS architecture for enterprise or regulated customers, including security questionnaires, SOC 2 or ISO 27001 audits, and SAML or OIDC identity federation.
Agentic AI infrastructure experience, including tool and skill protocols, sandboxed execution, evaluation frameworks, cost and latency control, and Amazon Bedrock or comparable platforms.
Experience with event-sourced or bitemporal data architectures and versioning schemas and data together.
Background in biopharma, preclinical research, or regulated environments such as GLP, IND-enabling studies, or FDA submissions.
Hardware-adjacent software experience, including telemetry ingestion, IoT fleets such as AWS IoT Greengrass, lab automation, or robotics integration.
Advanced degree (MS or PhD) in computer science, applied mathematics, computational biology, or a related field.

Responsibilities

Own the end-to-end architecture of the LIMS and its Cortex and NeuroscaleOps applications, including web front ends, APIs, backend data models, and pipelines connecting them to the datalake.
Work with scientists, perfusionists, and robotics engineers to understand experiment design and encode that knowledge as ontologies and schemas.
Design and deliver experiment-design user experiences, including protocol templates, dosing and sampling plans, plate and slice layouts, point-of-entry validation, and design-version diffs.
Build and operate an LLM-assisted ontology pipeline with versioning, human approval gates, and regression tests.
Lead the re-architecture of Neurolens as a multi-tenant AWS platform and own its licensing-aware permissions model.
Enable partner contributions of data and tools in a second phase, with validation, provenance, and isolation guarantees.
Establish provenance capabilities including a governed skills and tools registry, immutable run records, deterministic re-execution, and regulatory-review exports.
Scale execution with per-tenant and per-run cost attribution, and partner with the Head of AI on evaluation of correctness and reproducibility.
Own production infrastructure, including infrastructure as code, CI/CD, observability, and operational practices suitable for systems used during experiments on irreplaceable tissue.
Evolve datalake data models alongside the LIMS so physiological telemetry, imaging, and omics data can be joined based on experiment design.
Maintain security and compliance controls across tenants, including least privilege, encryption, and audit logging.
Serve as Bexorg’s senior technical authority for application and cloud architecture, setting standards for design, code review, testing, and documentation.
Mentor engineers and scientists who build tools with LLMs.
Represent Bexorg’s software platform to biopharma partners, foundation partners, and government grantors.
Communicate with technical and non-technical stakeholders and produce design documents, decision records, and runbooks.