Bioinformatics Software Engineer

ACL Digital; Foster City (CA); Hybrid; USD 92,000 - 99,000; Full time

Job summary

ACL Digital seeks a Bioinformatics Software Engineer to contribute to a next-generation computational platform for antibody design and assessment. You will build scalable software infrastructure, automated science workflows, data management, and interactive visualization.

The role requires strong Python, FastAPI, and pipeline orchestration experience, with exposure to HPC and cloud environments, and collaboration within multidisciplinary teams. Hybrid onsite work in Foster City, CA is expected.

Qualifications

• Bachelor’s or Master’s degree in Computer Science, Bioinformatics, Computational Biology, Physics, or a related field.
• Strong proficiency in Python and scientific software development.
• Hands-on experience with FastAPI, SQL/NoSQL databases, and database design.
• Experience developing and orchestrating automated computational pipelines, preferably using Nextflow or similar workflow frameworks.
• Experience with HPC environments and workload schedulers such as SLURM.
• Experience with Git, containerization technologies such as Docker, and modern software development practices.
• Experience with cloud platforms such as AWS or GCP.
• Excellent communication and collaboration skills within multidisciplinary scientific teams.

Responsibilities

• Design and implement scalable, web-based interfaces for computational biophysics and antibody design workflows.
• Develop and optimize database schemas to manage scientific data, computational results, and associated metadata.
• Build and maintain FastAPI-based backend services and APIs supporting computational workflows.
• Develop and orchestrate automated scientific pipelines using tools such as Nextflow, containers, and SLURM.
• Build software connecting databases, computational pipelines, APIs, and interactive visualization tools.
• Use modern AI-assisted development and vibe-coding approaches to rapidly prototype, test, and iterate on scientific applications.
• Ensure code quality through modular design, version control, testing, documentation, and maintainability.
• Support platform deployment and testing in HPC and cloud-based environments.

Skills

Python

SQL/NoSQL

FastAPI

Git

Docker

Nextflow

SLURM

AWS

GCP

HPC

Communication

Education

Bachelor’s or Master’s degree in CS/Bioinformatics/Computational Biology

Tools

Docker

Nextflow

SLURM

AWS

GCP

FastAPI

Job description

Job Title: Bioinformatics Software Engineer

Location: Foster City, CA 94404

Type of Position: Only on W2 basis

Hybrid 3 days onsite - Local Candidates Only.

Position Summary

• Client is seeking a highly motivated Bioinformatics Software Engineer to contribute to the development of a next-generation computational platform for antibody-based therapeutic design and assessment.
• This contractor role will focus on building scalable software infrastructure, automated scientific workflows, data management, and interactive visualization.
• The ideal candidate will have strong expertise in scientific software development, workflow orchestration, backend and web development, database design, and HPC/cloud computing.

Key Responsibilities

• Design and implement scalable, web-based interfaces for computational biophysics and antibody design workflows.
• Develop and optimize database schemas to manage scientific data, computational results, and associated metadata.
• Build and maintain FastAPI-based backend services and APIs supporting computational workflows.
• Develop and orchestrate automated scientific pipelines using tools such as Nextflow, containers, and SLURM.
• Build software connecting databases, computational pipelines, APIs, and interactive visualization tools.
• Use modern AI-assisted development and vibe-coding approaches to rapidly prototype, test, and iterate on scientific applications.
• Ensure code quality through modular design, version control, testing, documentation, and maintainability.
• Support platform deployment and testing in HPC and cloud-based environments.

Required Qualifications

• Bachelor’s or Master’s degree in Computer Science, Bioinformatics, Computational Biology, Physics, or a related field with 0–3 years of relevant experience. PhD candidates are also welcome to apply.
• Strong proficiency in Python and scientific software development.
• Hands‑on experience with FastAPI, SQL/NoSQL databases, and database design.
• Experience developing and orchestrating automated computational pipelines, preferably using Nextflow or similar workflow frameworks.
• Experience with HPC environments and workload schedulers such as SLURM.
• Experience with Git, containerization technologies such as Docker, and modern software development practices.
• Experience with cloud platforms such as AWS or GCP.
• Excellent communication and collaboration skills within multidisciplinary scientific teams.

Preferred Qualifications

• Familiarity with protein structure, antibody design, molecular modeling, or structure-based computational methods.
• Familiarity with molecular modeling or protein structure tools such as MOE, Schrödinger, or equivalent.
• Experience applying AI-assisted coding tools to accelerate scientific software development and prototyping.
• Knowledge of antibody developability or biologics discovery workflows.
• Prior experience in biotech or pharmaceutical industry settings.

The pay rate ranges from $67/hr - $72/hr on W2