Bioinformatics Pipeline Engineer

Bioinformatics Pipeline Engineer W2 Contract Pay Rate: $60 - $70 per hour Location: Redwood City, CA - Remote Role Job Summary: In this role, you will work between the data and data analysts in the Translational Medicine group, developing analytical pipelines, automating scripts, and disseminating biomarker data from clinical trial samples. This data consists of a diverse mix of tissue and blood analyses with associated variant calls, imaging, and other molecular assay outputs. The bioinformatics pipeline engineer will work on various projects in different phases of drug development and contribute to the cross-functional bioinformatics team, which includes other bioinformaticians and data scientists. Duties and Responsibilities:

• Convert experimental analysis scripts from scientists into robust, reproducible, and standardized workflows.
• Assist in the maintenance and development of a large multi-user Python analytical framework
• Work to automate testing, deployment, and version control to ensure data integrity and correct execution of outputs.
• Work with molecular biologists and IT teams to refine analysis requirements and troubleshoot failures.
• Carry out data modeling and curation to ensure data quality and relevance.
• Collaborate with other departments to share and disseminate data in a controlled and documented manner.
• Develop web-based data visualization dashboards using Python and R frameworks.

Requirements and Qualifications:

• Ph. D/Master's or Bachelor's degree with 4+ years of experience in biology/computer science-related field.
• Proficient in developing and maintaining Python packages
• Skilled in using R for data manipulation and analysis.
• Expertise in using Linux clusters, cloud computing, and file systems.
• Familiar with professional software development systems (git, IDEs, environments, packaging, and deployment)
• Proficient in designing and querying databases using SQL and object-relational mapping techniques.
• Strong familiarity with bioinformatics data types and outputs.
• Excellent communication skills, enabling effective collaboration and conveying technical information clearly to diverse audiences.

Preferred Qualifications:

• Experience using visualization packages such as R Shiny, Power BI, or similar systems.
• Experience in biomarker data analysis and bioinformatics.
• Familiarity with large genomic data sets (GDC, TCGA, etc.).
• Experience in tools to analyze cancer genomics datasets (GATK, Salmon, OncoKB, VEP, etc.).
• Development experience in groups using IDEs, a ticketing system, and software control systems (GIT).

Desired Skills and Experience Bioinformatics, Pipeline Development, Analytical Pipelines, Workflow Automation, Reproducible Workflows, Python, Python Packages, R, Data Manipulation, Data Analysis, Linux Clusters, Cloud Computing, File Systems, Git, Version Control, IDEs, Software Environments, Packaging, Deployment, Automated Testing, SQL, Database Design, Database Querying, Object-Relational Mapping, Data Modeling, Data Curation, Biomarker Data, Clinical Trial Samples, Translational Medicine, Molecular Assay Data, Variant Calls, Tissue Analysis, Blood Analysis, Imaging Data, Bioinformatics Data Types, Genomic Data Sets, Cancer Genomics, GDC, TCGA, GATK, Salmon, OncoKB, VEP, R Shiny, Power BI, Web-Based Dashboards, Data Visualization, Data Dissemination, Data Integrity, Troubleshooting, Cross-Functional Collaboration, Molecular Biology, Drug Development, Communication Skills Bayside Solutions, Inc. is not able to sponsor any candidates at this time. Additionally, candidates for this position must qualify as a W2 candidate. Bayside Solutions, Inc. may collect your personal information during the position application process. Please reference Bayside Solutions, Inc.'s CCPA Privacy Policy at www.baysidesolutions.com.