Job Description

Job Summary

We are seeking a Python/SQL Developer with expertise in AWS RDS-hosted PostgreSQL to design and implement a system that integrates Benchling Electronic Lab Notebook (ELN) data and other laboratory instrument outputs into a structured PostgreSQL database. The ideal candidate will be responsible for developing ETL pipelines, optimizing database performance, and ensuring secure and scalable cloud-based data storage.

This role will involve:

• Designing AWS RDS PostgreSQL database schemas.
• Building Python-based ETL pipelines to extract, transform, and load (ETL) data from Benchling ELN, laboratory instruments, and other sources.
• Implementing API integrations and optimizing query performance for scientific data analysis.

Key Responsibilities

Database Design & AWS RDS Management

• Design and develop an AWS RDS-hosted PostgreSQL database to store structured lab data.
• Define schemas, tables, indexes, constraints, and stored procedures for efficient querying.
• Implement best practices for database security, backup, and performance tuning in AWS RDS.
• Set up automated scaling, monitoring, and failover strategies for high availability.

Data Integration & ETL Pipelines

• Develop Python-based ETL pipelines using SQLAlchemy, psycopg2, and AWS services (e.g., AWS Lambda, AWS Glue).
• Implement APIs and data connectors to retrieve and process data from Benchling ELN and lab instruments.
• Automate scheduled data ingestion jobs using AWS Step Functions, Airflow, or Prefect.

SQL Query Optimization & Performance Tuning

• Write and optimize PostgreSQL queries for high-performance data retrieval.
• Create materialized views, indexing strategies, and query caching.
• Monitor query execution plans using AWS RDS Performance Insights and optimize accordingly.

Data Quality, Validation, & Security

• Ensure data integrity, validation, and consistency across multiple lab data sources.
• Implement role-based access control (RBAC) and encryption for securing sensitive lab data.
• Use AWS IAM roles and VPC security groups to manage database access.

Collaboration & Documentation

• Work closely with scientists, bioinformaticians, and software engineers to integrate lab workflows into AWS RDS.
• Document data models, pipeline workflows, API integrations, and AWS RDS configurations.
• Provide training and support to users querying lab data.

Required Qualifications

Technical Skills

• Proficiency in Python (Pandas, SQLAlchemy, psycopg2, API requests).
• Strong SQL skills with expertise in PostgreSQL (functions, triggers, indexing, query optimization).
• Experience with AWS RDS (PostgreSQL), including:
• Setting up databases, read replicas, backups, and failover strategies.
• Using AWS IAM roles, VPCs, and parameter groups for security and performance.
• Monitoring database performance with AWS CloudWatch, RDS Performance Insights.
• Experience integrating with Benchling ELN API (GraphQL or REST).
• Familiarity with ETL frameworks.
• Experience working with scientific data formats (JSON, CSV, XML, Excel, instrument-generated data).
• Knowledge of AWS services (Lambda, S3, Step Functions) for cloud-based ETL processing.

Preferred Experience

• Ph.D. or equivalent experience in Computational Biology, Bioinformatics, Structural Biology, Machine Learning, or a related field
• Strong expertise in protein structure, function, and engineering, particularly in the context of antibodies
• Experience with machine learning, including deep learning frameworks (e.g., TensorFlow, PyTorch) and protein language model.
• Proficiency in programming languages such as Python, and experience with bioinformatics tools and databases
• Excellent problem-solving skills and the ability to work independently and collaboratively in a multidisciplinary environment
• Strong communication skills, with the ability to present complex scientific concepts to both technical and non-technical audiences
• Experience with high-throughput screening data and techniques for protein characterization.
• Familiarity with concepts in immunology and antibody therapeutics

Soft Skills

Strong problem-solving skills and ability to work with scientists, engineers, and IT teams.

Ability to manage multiple data sources and ensure integration consistency.

Strong written and verbal communication skills for documentation and user training.

About Prellis Biologics

At Prellis we integrate human biology with machine learning. We aim to revolutionized drug discovery by harnessing the power of human immune system with tightly, integrated machine learning to develop next-generation antibody therapeutics with unparalleled speed, precision and safety. We are committed to empowering our pharmaceutical partners with access to the most promising fully human body candidate rapidly identified from the human immune repertoire, enabling them to bring life-changing treatments to patients faster than ever before. Prellis Biologics is a pre-IPO biotech located in Berkeley CA with a team-oriented, inclusive, and family-friendly culture. Our growing pipeline target high unmet patient needs across therapeutics including metabolic, inflammation, and oncology disease. Prellis has raised funding from top investors, including Celesta, Khosla Ventures, SOSV, & Avidity Partners.

What you can expect of us

As we work to develop treatments that take care of others, we also work to care for your professional and personal growth and well-being. From our competitive benefits to our collaborative culture, we’ll support your journey every step of the way.

The expected annual salary range for this role in the U.S. is posted. Actual salary will vary based on several factors including but not limited to, relevant skills, experience, and qualifications.

Application deadline

Prellis does not have an application deadline for this position; we will continue accepting applications until we receive a sufficient number or select a candidate for the position.

Prellis Bio is an equal opportunity employer. All applicants will be considered for employment without attention to race, color, religion, sex, sexual orientation, gender identity, national origin, veteran or disability status.

We believe diversity, equity, and inclusion need to be at the foundation of our culture. We work hard to bring together diverse teams–grounded in a wide range of expertise and life experiences–and work even harder to ensure those teams thrive in inclusive, growth-oriented environments supported by equitable company and team practices. All candidates can expect equitable treatment, respect, and fairness throughout the interview process.

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