Software Engineer — Agentic data pipelines

Iambic; San Diego (CA); On-site; USD 110,000 - 162,000; Full time

Benefits offered by this job

Company paid healthcare

401K matching

Uncapped vacation

Flexible spending accounts

Voluntary life insurance

Job summary

Iambic Therapeutics is seeking a software engineer to design agentic systems that turn biomedical data sources into reviewed, versioned datasets for Enchant, the multimodal transformer. You will build pipelines that can generate code to acquire, clean, format, and quality-check large-scale data and produce auditable reports.

You will work at the intersection of AI-driven automation and biomedical data engineering, focusing on reliability, security, and reproducibility in a production setting.

Qualifications

• Master’s degree in a computational STEM field, or a Bachelor’s with 2+ years of industry experience.
• Strong Python engineering skills with production-quality software experience.
• Hands-on experience with LLM APIs and agentic patterns.
• Familiarity with biomedical or chemical data formats and sources.
• Fundamentals of ETL, data validation, and working with structured/unstructured data.
• Experience with Python testing frameworks such as pytest.

Responsibilities

• Design, build, and maintain agentic systems turning data sources into reviewed, versioned datasets.
• Develop LLM-based data cleaning, normalization, and formatting pipelines.
• Implement automated quality-control workflows to detect anomalies and enforce standards.
• Collaborate with ML scientists to translate data requirements into scalable systems.
• Monitor distributed data pipelines in production and improve robustness.
• Document provenance, processing decisions, and quality metrics for reproducibility.

Skills

Python

LLM APIs

Agentic patterns

Data engineering

Pytest

Biomedical data

Cloud (AWS)

Kubernetes

Security best practices

Large-scale datasets

Education

Master’s degree or Bachelor + 2+ years

Tools

GPT/Claude APIs

Docker

Job description

Job Summary

We are seeking a software engineer to join our team at Iambic Therapeutics, working on data acquisition and curation for Enchant, our multimodal transformer model trained at scale on a wide variety of biomedical data. In this role, you will design and build agentic systems that generate code to acquire, clean, format, quality-control, and generate auditable data reports for the large-scale datasets that power Enchant training. The model writes the code, the code runs the pipeline. You will work at the intersection of LLM-based automation and biomedical data engineering - developing AI agents that can navigate heterogeneous data sources, enforce quality standards, and operate reliably at scale.

This role is ideal for candidates who combine strong software engineering instincts with scientific understanding of biomedical data, and who are excited about using LLMs as tools to solve practical data problems.

Key Responsibilities

• Design, build, and maintain agentic systems that turn a pointer to a biomedical data source (web page, S3 path, GitHub repository, a table in a paper) into a reviewed, versioned dataset. The agent's output is committed pipeline code and its test suite, so re-running it later reproduces the same dataset. Develop LLM-based pipelines for data cleaning, normalization, and formatting across diverse data modalities (e.g., molecular, genomic, clinical, literature)
• Implement automated quality-control workflows that detect anomalies, flag inconsistencies, and enforce data standards
• Evaluate and iterate on agent architectures, prompting strategies, tool definitions, validation loops, and evaluation harnesses that make agent-generated code trustworthy, improving reliability and throughput over time
• Collaborate with ML scientists on the Enchant team to understand data requirements and translate them into scalable acquisition and processing systems
• Monitor and maintain distributed data pipelines in production, diagnosing failures and improving robustness over time
• Document data provenance, processing decisions, and quality metrics to support reproducibility and auditing
• Operate the agents safely with sandboxed execution, least-privilege credentials, restricted network access, audit logs, and raising potential security risks to the team

Qualifications

• Master’s degree in a computational STEM field, or a Bachelor’s with 2+ years of industry experience
• Strong Python engineering skills, including experience building and maintaining production-quality software
• Hands-on experience with LLM APIs (e.g., Claude, GPT) and agentic patterns such as tool use, orchestration, and multi-step reasoning
• Familiarity with biomedical or chemical data sources and formats (e.g., PDB, UniProt, ChEMBL, SDF/MOL, FASTA, or similar)
• Comfort with data engineering fundamentals: ETL design, data validation, and working with structured and unstructured data at scale
• Hands-on experience with Python testing frameworks (e.g., pytest fixtures, parametrization)

Preferred Qualifications

• Experience with agent orchestration frameworks, and with evaluation harnesses for LLM-generated code
• Familiarity with cloud infrastructure and workflow orchestration (e.g., AWS, Docker, Kubernetes)
• Knowledge of multimodal biomedical data - spanning small molecules, proteins, assays, images, 'omics', and/or clinical records
• Experience with large-scale dataset construction or curation for ML model training
• Knowledge of agent security practices: sandboxing, scoped credentials, prompt injection
• Interest in a longer-term project: a natural language orchestrator that lets drug prosecution team members request inference, fine-tuning, virtual screens, and dataset analysis without writing code using our internal tools

About Iambic Therapeutics

Iambic is a clinical-stage life-science and technology company developing novel medicines using its AI-driven discovery and development platform. Based in San Diego and founded in 2020, Iambic has assembled a world-class team that unites pioneering AI experts and experienced drug hunters. The Iambic platform has demonstrated delivery of new drug candidates to human clinical trials with unprecedented speed and across multiple target classes and mechanisms of action. Iambic is advancing a pipeline of potential best-in-class and first-in-class clinical assets, both internally and in partnership, to address urgent unmet patient need. Learn more about the Iambic team, platform, pipeline, and partnerships at iambic.ai.

MISSION & CORE VALUES

Our mission is to deliver better medicines through innovations in AI-based discovery technologies. The culture and work at Iambic Therapeutics are profoundly strengthened by the diversity of our people and our differences in background, culture, national origin, religion, sexual orientation, and life experiences. We are committed to building an inclusive environment where a diverse group of talented humans work together to discover therapeutics and create technologies.

Pay And Benefits

We offer industry leading competitive pay, company paid healthcare, flexible spending accounts, voluntary life insurance, 401K matching, and uncapped vacation to our team. We are in a brand-new state-of-the-art facility in beautiful San Diego with an onsite gym, dining, and easy access to great places to live and play.

Compensation Range: $110K - $162K