Prellis Biologics, Inc.
Python-SQL Developer - AWS RDS PostgreSQL-Lab Data Integration Bioinformatics Be
Prellis Biologics, Inc., Berkeley, California, United States, 94709
Contract Bioinformatics Role
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:
Building Python-based ETL pipelines to extract, transform, and load (ETL) data from Benchling ELN, laboratory instruments, and other sources.
Key Responsibilities
Database Design & AWS RDS Management
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. 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
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. 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. Required Qualifications
Strong SQL skills with expertise in PostgreSQL (functions, triggers, indexing, query optimization). Experience with AWS RDS (PostgreSQL), including setup, backups, failover strategies, security using IAM roles, VPCs, parameter groups, and performance monitoring. Experience integrating with Benchling ELN API (GraphQL or REST). Familiarity with ETL frameworks and scientific data formats (JSON, CSV, XML, Excel). Knowledge of AWS services (Lambda, S3, Step Functions) for cloud ETL processing. Preferred Experience
Ph.D. or equivalent in Computational Biology, Bioinformatics, Structural Biology, Machine Learning, or related fields. Experience with machine learning frameworks (e.g., TensorFlow, PyTorch) and protein language models. Proficiency in Python and experience with bioinformatics tools and databases. Excellent problem-solving skills and ability to work independently and in multidisciplinary teams. Strong communication skills for presenting complex scientific concepts. Experience with high-throughput screening data and immunology/antibody therapeutics concepts. Soft Skills
Strong problem-solving skills and ability to collaborate with scientists, engineers, and IT teams. Excellent written and verbal communication skills for documentation and training. Prellis aims to revolutionize drug discovery by integrating human biology with machine learning, developing next-generation antibody therapeutics rapidly and safely. We are committed to diversity, equity, and inclusion, fostering an inclusive environment where all candidates are treated fairly throughout the hiring process. Salary Range:
$128,000 - $168,000 per year, based on experience and qualifications. Join Our Team
Fill out the application form to start your journey with us.
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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. 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
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. 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. Required Qualifications
Strong SQL skills with expertise in PostgreSQL (functions, triggers, indexing, query optimization). Experience with AWS RDS (PostgreSQL), including setup, backups, failover strategies, security using IAM roles, VPCs, parameter groups, and performance monitoring. Experience integrating with Benchling ELN API (GraphQL or REST). Familiarity with ETL frameworks and scientific data formats (JSON, CSV, XML, Excel). Knowledge of AWS services (Lambda, S3, Step Functions) for cloud ETL processing. Preferred Experience
Ph.D. or equivalent in Computational Biology, Bioinformatics, Structural Biology, Machine Learning, or related fields. Experience with machine learning frameworks (e.g., TensorFlow, PyTorch) and protein language models. Proficiency in Python and experience with bioinformatics tools and databases. Excellent problem-solving skills and ability to work independently and in multidisciplinary teams. Strong communication skills for presenting complex scientific concepts. Experience with high-throughput screening data and immunology/antibody therapeutics concepts. Soft Skills
Strong problem-solving skills and ability to collaborate with scientists, engineers, and IT teams. Excellent written and verbal communication skills for documentation and training. Prellis aims to revolutionize drug discovery by integrating human biology with machine learning, developing next-generation antibody therapeutics rapidly and safely. We are committed to diversity, equity, and inclusion, fostering an inclusive environment where all candidates are treated fairly throughout the hiring process. Salary Range:
$128,000 - $168,000 per year, based on experience and qualifications. Join Our Team
Fill out the application form to start your journey with us.
#J-18808-Ljbffr