Senior Scientist, Full Stack Developer/Software Engineer - Protein Design

$113,000 - $195,500/Yr

Johnson & Johnson - Harrisburg, PA

Full-time - Senior

Remote - Harrisburg, PA

Chemical Manufacturing

About the position

Janssen Research & Development, L.L.C., a division of Johnson & Johnson's Family of Companies, is seeking a Senior Scientist, Full Stack Developer/Software Engineer - Protein Design. This role is pivotal within the Therapeutics Discovery organization, focusing on spearheading in silico molecular design and simulation initiatives that support and accelerate the drug discovery and development pipeline of protein-based therapeutics. The position is based at our JRD site in either Spring House, PA or Cambridge, MA, with remote work options considered on a case-by-case basis. In this role, you will collaborate closely with a passionate team of scientists and engineers, contributing to the development and maintenance of highly scalable protein design and modeling infrastructures. You will be responsible for building web-based applications that facilitate intuitive access to our protein design platforms and software tools for multi-functional teams across Johnson & Johnson. Your work will also involve the development of innovative machine learning models that support research and development in protein design, structural modeling, and attribute predictions, enabling multi-property optimization and de-novo design. Your expertise will bridge the gap between computational biology and software engineering, utilizing your extensive coding skills, cloud computing knowledge, and familiarity with machine learning architectures to drive groundbreaking discoveries in protein therapeutics. This role is essential in delivering unique molecules and expediting the discovery of protein therapeutics across various modalities and indications, including protein, gene, and cell therapy.

Responsibilities

• Apply infrastructure as code (IaC) tools, such as Terraform, to automate and run cloud resources efficiently and effectively.
• Employ extensive coding skills in Python to develop software tools and pipelines critical to therapeutic discovery.
• Develop and maintain web applications that enable intuitive access to our protein design platforms and software tools for multi-functional teams across J&J.
• Develop and fine-tune ML models to support innovative research and development in protein design, structural modeling, and attribute predictions to enable multi-property optimization and de-novo design.
• Integrate and lead deployment of workflow systems like Flyte, Nextflow, or Airflow to streamline the execution of sophisticated design, modeling, and ML tasks as well as automated data processing DevOps pipelines.
• Contribute to general DevOps practices, including continuous integration/continuous deployment (CI/CD) pipelines, monitoring, logging, and incident response, to ensure high availability and performance of our platforms.

Requirements

• PhD in Biomedical Engineering, Biochemistry, Computational Biology, Computer Science, Structural Biology, Biophysics, Material Science, or other related quantitative field with at least 3 years of experience is required.
• Or MSc in Biomedical Engineering, Biochemistry, Computational Biology, Computer Science, Structural Biology, Biophysics, Material Science, or other related quantitative field with at least 5 years of experience is required.
• Extensive knowledge of cloud compute infrastructure is required, with demonstrated AWS experience strongly preferred.
• Experience with infrastructure as code (IaC) tools, such as Terraform, is preferred.
• Demonstrable experience in high-performance computing (HPC) environments, with the ability to optimize and manage computational workflows for bioinformatics and machine learning tasks is preferred.
• Broad experience in DevOps practices is required, including automation, CI/CD, containerization (e.g., Docker, Kubernetes), monitoring, and incident management.
• Extensive expertise in Python is required, with a track record of developing sophisticated software solutions in a scientific or research context preferred.
• Strong front-end development skills and a solid understanding of user experience (UX) principles and web development frameworks, particularly in creating complex web apps is required.
• Familiarity with workflow management systems such as Nextflow, Airflow, or Snakemake (or similar) frameworks to support scalable and reproducible research pipelines preferred.
• Solid understanding of machine learning infrastructures, including experience with large language models, convolutional neural networks, and classic ML algorithms such as Catboost or XGBoost are preferred.

Nice-to-haves

• Direct experience in training ML models for scientific research is a plus.

Benefits

• Medical, dental, vision, life insurance, short- and long-term disability, business accident insurance, and group legal insurance.
• Consolidated retirement plan (pension) and savings plan (401(k)).
• Vacation - up to 120 hours per calendar year.
• Sick time - up to 40 hours per calendar year; for employees who reside in the State of Washington - up to 56 hours per calendar year.
• Holiday pay, including Floating Holidays - up to 13 days per calendar year.
• Work, Personal and Family Time - up to 40 hours per calendar year.