Job description
Job Functions, Duties, Responsibilities and Position Qualifications:
POSITION TITLE: Senior Bioinformatics-Clinical Database Developer
STANDARDIZED JOB TITLE: Database Development, Web Application Development, and Clinical Analytics
EXEMPT STATUS: Exempt
POSITION SUMMARY:
Sr. Database Developer works with cross-functional groups & Medical Leadership for developing a databases for a clinical assays. The candidate is expected to have strong expertise with relational databases, web development and Programing in clinical/bioinformatics areas preferably in a CLIA/CAP setting. This full FTE position is an on-site position at the SHUSA-ThyroSeq Laboratory (760 Westchester Avenue, Rye Brook, 10573).
Requirements:
- Strong expertise with relational databases (PostgreSQL/MySQL) and SQL, Python, programming with Python, R Shell required.
- Expertise in web development tools (such as JavaScript/Jquery/ Chrome DevTools/NPM) and web-framework including Django, R Shiny.
- Ability to create APIs using data from the databases, understanding of data normalization w.r.t. to database development.
- Expert level of Linux operating systems and a programming language such as Phyton, Javascript/C++/HTML/CSS, node.js (required)
- Skills and experience with integrating web and clinical databases, and/or genomics/genetics data management preferred.
- Experience with Laboratory Information Management Systems (LIS/LIMS) (nice to have)
- Ability to create new database(s), troubleshoots, and updates programs as needed to support the design, development, and implementation for analyzing and reporting clinical data.
- Collaborates with Bioinformatics programmers and developers on the scripting, design, testing, migrations and implementation of project database based on department needs.
- Develops progress and custom reports to help the team ensure timelines and quality expectations are met.
- Participates in user acceptance testing and validation activities.
- Works effectively with cross-functional groups, clinical teams, and vendors.
- Experience working with high-performance computing environments and job-schedulers such as Slurm, LSF or PBS. Familiarity with container technologies such as docker and singularity. (preferred)
- Knowledgeable on best practices for the full software development life cycle, including coding standards, code reviews, source control management (Git), build processes, and operations.
- Exposure in analysis of Next-Generation Sequencing (NGS) datasets (from Ion-Torrent and Illumina), especially in oncology panels and for tumor normal pair analysis (nice to have)
- Well versed in publically available clinical and genomic databases for data retrievals.
- Experience with NGS based bioinformatics tools (nice to have)
- Strong analytical and organizational skills.
- Good written and oral communication skills (required). Familiarity of discussing complex technical issues with non-technical people (nice to have).
- Ready to lead database generation efforts, with ability to attend timelines, generate statistics, prepare ghant charts, plotting, and manage the project with various stakeholders with minimum supervision.
- Works effectively with an interdisciplinary team of Bx scientists, IT, physicians, genetic counselors, and molecular lab staff.
- High degree of professionalism, enthusiasm, and initiative in a fast-paced environment
- Attention to details is critical so as appropriate documentation and regular presentation.
Responsibilities:
- Responsible for planning and executing clinical database infrastructure activities in clinical studies. Develop and maintain specific in house database applications, deployment, including automation, testing, and virtualization and container technology
- Generates, troubleshoots and maintains the databases that allows communication with LIMS, NGS pipeline, and related tools used in the lab to capture various data, including demographics, billing, NGS QC metrics, turnaround time, confirmatory and clinical test results during the journey of the specimen.
- Works to provide expertise in the development and maintenance of database development standard operating procedures (SOPs) and best practices
- Compiles steps of the generation of the database and documents them.
- Writes and maintains SOPs related to database generation compliant at all times per CAP/CLIA NYSDOH requirements.
- Follows all the Sonic Healthcare USA’s measures to secure the data generated, especially PHI.
- Ensures that all activities under responsibility are properly documented (traceability of changes, data specifications, SOPs) according to the internal guidance documents.
- Performs advanced analysis and review of NGS results from targeted panel or whole "omics" testing, including QC metrics, variant review, variant annotation, and variant classification.
- Works collaboratively with technical, bioinformatics, and clinical sign-out teams to enhance workflow efficiency and robustness.
- Participates in technical and professional Quality Improvement initiatives.
- Participates in clinical test development, including assessment of platforms and scope of project.
- Outlines plans, executes the studies and summarizes the verification and/or validation data.
- Performs in accordance with system-wide competencies/behaviors.
- Performs other clinical and or research duties as assigned.
- Involves in team building efforts, and interviews.
Department: Bioinformatics /ThyroSeq
Reports To: Director, Bioinformatics
POSITION(S) SUPERVISED: None
CAREER PATH OPPORTUNITIES: TBD
POSITION QUALIFICATIONS:
- DB/ Software/programming languages: PostgreSQL, SQL, Python, DJANGO, R, Bioconductor, Shiny, HTML, CSS Node.JS and Shell scripting
- Operating systems, Linux, Mac, Windows
EDUCATION & EXPERIENCE:
- MS degree in Bioinformatics, IT, or Computer Sciences (CS), Computational Biology, with at least 5 years of experience in a clinical/Bioinformatics database & web development
Scheduled Weekly Hours:
40
Work Shift:
Company:
CBL Path, Inc.
Sonic Healthcare USA provides equal employment opportunities to all employees and applicants for employment and prohibits discrimination and harassment of any type without regard to race, color, religion, age, sex, national origin, disability status, genetics, protected veteran status, sexual orientation, gender identity or expression, or any other characteristic protected by federal, state or local laws.
This policy applies to all terms and conditions of employment, including recruiting, hiring, placement, promotion, termination, layoff, recall, transfer, leaves of absence, compensation and training.
offroadmanagementgroup.com is the go-to platform for job seekers looking for the best job postings from around the web. With a focus on quality, the platform guarantees that all job postings are from reliable sources and are up-to-date. It also offers a variety of tools to help users find the perfect job for them, such as searching by location and filtering by industry. Furthermore, offroadmanagementgroup.com provides helpful resources like resume tips and career advice to give job seekers an edge in their search. With its commitment to quality and user-friendliness, offroadmanagementgroup.com is the ideal place to find your next job.