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Senior Bioinformatics Scientist

Company: Jobot
Location: Carlsbad
Posted on: November 23, 2021

Job Description:

Join THE Team! Develop & Design Novel Technologies!This Jobot Job is hosted by: Nick RogersAre you a fit? Easy Apply now by clicking the "Apply Now" button and sending us your resume.Salary: $130,000 - $170,000 per yearA bit about us:We're focused on developing and designing novel technologies that identify an individual's risk of disease before they become sick. Through the discovery and conversion of biological signals into predictive, contextual health insights, we are empowering patients and their healthcare providers with objective, actionable information to prevent disease. We need you to help us achieve our lofty goals!Why join us?

  • Competitive Salary
  • Complete Benefits Package
  • Hybrid/Remote work schedule
  • Cutting Edge Technology
  • Career Growth!Job DetailsJob Description SummaryThe Senior Bioinformatics Scientist will provide software engineering and machine learning operations support needed for core bioinformatics functions within our company. You will play a critical role in enabling a new automated bioinformatics software workflows and machine learning operations paradigm for us that includes next-generation sequencing and advanced bioinformatics techniques to deliver individualized colorectal cancer and other metagenomic and genomic-based diagnostic assays to patients. You will be expected to take ownership, provide guidance and feedback on bioinformatics software development, machine learning operations (MLOps), and deployment to multi-disciplinary and cross-functional teams. Essential Functions
    • Ensure alignment of bioinformatics software milestones with those of the broader team.
    • Review and refact legacy bioinformatics code (in Python, R, and shell scripting language) according to best software practices.
    • Test and deploy a variety of bioinformatics pipelines into a production environment. (e.g. Next Flow, Docker, GitHub, MLFlow, and DVC).
    • Test and deploy cloud-based database management and MLOps technology, platforms, and pipeline such as AWS, GCP, Azure, AWS. Jupyter Notebooks, Git SQL, and bash shell scripts.
    • Create automation pipelines for the entire MLOps lifecycle from data prep, training, deployment, and monitoring.
    • Contribute to software engineering/QA aspects of the production bioinformatics pipelines.
    • Select, evaluate, and integrate industry leading tools and frameworks.
    • Develop efficient, maintainable, and documented code production software from scientific prototype code using software development best practices.
    • Collaborate with data scientists, DevOps engineers, translational scientists, physicians, pathologists, and clinical trial operations and supporting transdisciplinary teamwork using cloud-based Microsoft Teams and Asana project management, systems integration, and collaboration platforms.
    • Communicate technical information to both technical and non-technical collaborators: you identify core challenges in complex situations, explain trade-offs, and incorporate feedback to make decisions using code reviews, docs, wikis, meetings, and other channels as needed.
    • Lead MLOps core components of scientific and diagnostic assay product development roadmap concerning high-throughput online inference, active learning for unsupervised and supervised ML approaches, and reproducible ML pipelines at scale.
    • Refine and improve end-to-end software and machine learning workflows using industry best practices.
    • Design, build and manage processes to deploy production models in batch (offline) and real-time (online) inference environments.
    • Develop strategies and solutions to monitor model performance & quality over time measuring and optimizing the performance of model training and inference workloads, and train and test models at-scale.Competencies
      • Experience building pipelines using workflow engines and workflow languages.
      • Familiar with the basic principles in bioinformatics, genomics and NGS technology.
      • Experience shipping code in a clinical production environment.
      • Passionate about rigorous engineering practices and discipline: code reviews, automated testing, logging, monitoring, alerting, etc.Required Education and Experience
        • Bachelor of Science in computer science or related field, with a minimum of 5 years of experience in software development within an industry setting; or
        • Master of Science in computer science, with a minimum of 2 years of experience in software bioinformatics, computer science, multivariate statistics, biostatistics, or a combination of related fields, with substantial experience and record of accomplishments in applied software development within the life sciences industry or medical research center setting.
        • Exceptional coding skills in Python, R, and other applicable programing languages preferably in the context of bioinformatics and health diagnostics applications.
        • Knowledge and proficiency in designing, deployment, query authoring, and management of local and cloud-based SQL and other relational databases.
        • Experience with developing, integrating, deploying, and testing production software (preferably bioinformatics, machine learning, multivariate statistics, and data visualization software).
        • Experience in preparing and reviewing Software Requirements and Specifications (SRS), especially in the context of biomedical software. Knowledge and experience of good software engineering practices (e.g., CI/CD, source control, testing, instrumentation/logging, security, data privacy, etc.)
        • Experience with developing in cloud environments (AWS, Azure, GCP) using Docker, Next Flow, Data Robot, or other containerization and life-cycle deployment packages.Preferred Experience
          • Strong understanding of software quality assurance is a plus.
          • Prior substantial experience using and developing bioinformatics, machine learning, and health diagnostic assay pipelines is a plus.
          • Proven MLOps life-cycle experience with mastery of a relevant software and platform programming and containerization languages such as Python, R, Docker, Perfect, and Kubernetes.
          • Experience using open-source machine learning and deep learning frameworks (e.g. Scikit-learn, Tensorflow/Keras, SparkML, Databricks, Data Robot).
          • Proven experience with one the major cloud platforms AWS, GCP, Azure, DataRobot, or others.Work EnvironmentThis position is based in Carlsbad, CA with remote work flexibility.Interested in hearing more? Easy Apply now by clicking the "Apply Now" button.

Keywords: Jobot, San Diego , Senior Bioinformatics Scientist, Other , Carlsbad, California

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