Bioinformatics Engineer III (Loughnan) (Finance)

Position Summary

The Bioinformatics Engineer III is responsible for designing, operating, supporting, maintaining, developing, integrating, and deploying bioinformatics tools and software supporting the scientific mission of the JCVI. Bioinformatics Engineer III contributes to all phases of the software engineering lifecycle to maintain JCVI's scientific leadership through the cost-effective application of bioinformatics and software engineering tools and techniques to solve JCVI's bioinformatics challenges. May supervise entry level analysts or engineers.

Essential Functions

• Designs and supports the full software development lifecycle as well as operations for software-based tools developed at JCVI, typically integrating COTS, or open-source software from 3^rd parties.
• Work extensively on ingesting, manipulating, performing quality control, aligning, and processing of large and complex datasets from various domains, e.g., whole genome sequencing data files (including fastq, fasta, bam, and vcf); brain imaging data (including DICOM and NifTi); wearable sensor data; geocoding data; tabulated behavioral and biospecimen data.
• Perform computational decontamination of oral microbe sequencing in human saliva sequencing samples.
• Executes bioinformatics assignments to meet project goals. Works independently where appropriate, exercising engineering judgment and involving supervisory personnel where appropriate. The Bioinformatics Engineer III assignments will be determined by management as a function of business requirements and personnel capabilities.
• Develops and maintains an understanding of the scientific and biological domain supported by the team, as well as bioinformatics tools, software, and IT technologies used by the team.
• Collaborates closely and effectively with software, bioinformatics, scientific, information technology, and administrative personnel within and outside the Venter Institute to accomplish goals. Is an effective member of software and multi-disciplinary teams.
• Complies with all documented JCVI policies and procedures. Works with manager and JCVI administrative functions to resolve issues as they arise.
• The dimensions upon which an Engineer's established capabilities and professional growth will be judged are based on the ability to:
  • Execute complex tasks effectively with limited supervision
  • Advance the level of software and bioinformatics technology used within the team
  • Provide project leadership and mentoring beyond the scope of their own work, including leadership of small ad-hoc project teams
  • Define and estimate scope of tasks prior to implementation
  • Execute projects within estimated time frames

• Responsible for the integration of environmental, health and safety protocols into work activities. This includes reporting potential hazards and when necessary helping to implement solutions to ensure safety and respect for the environment.
• Performs other duties as assigned.

• Strictly adheres to all documented JCVI policies and procedures to include carrying out all functions required of Institute employees (i.e. completion of timesheets in an accurate and timely manner).

Pre-Requisites

• BS, MS or PhD in Biology, Mathematics, Computer Science/Software Engineering (and a familiarity with the other discipline), or related disciplines is required
• Specific technical skills and experience pre-requisites will be established for each Bioinformatics Engineer position, and may include some combination of the following:
  • Data science and scripting languages (Python, R, shell) and associated tools
  • Relational database (Postgres, MySQL, Oracle, and related tools including SQL and PL/SQL) design, data warehousing, use and development of various APIs
  • Programming and software development best practices: testing, version control, dependency management, reproducible development environments, containerization (Docker/Singularity), continuous integration, etc.
  • Bioinformatics tools and techniques (GATK, IGV, snakemake, and other NGS software)
  • Web technologies (HTML, DHTML, XML, CSS, and JavaScript).
  • Operating Systems: UNIX and UNIX variants, Macintosh, and Cluster Computing (Sungrid and/or slurm)
• Strong written and verbal communication skills.
• Ability to collaborate across a multi-disciplinary team, and work independently.

Work Environment
The work environment characteristics described here are representative of those a teammate encounters while performing the essential functions of this job. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions.

• Moderate noise (i.e. business office with computers, phone, and printers, light traffic)
• Ability to work in a confined area.
• Ability to sit at a computer terminal for an extended period of time.

Physical Demands
The physical demands described here are representative of those that must be met to successfully perform the essential functions of this job. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions.

• While performing the duties of this job, the employee is regularly required to, stand, sit; talk, hear, and use hands and fingers to operate a computer and telephone keyboard reach, stoop kneel to install computer equipment
• Specific vision abilities required by this job include close vision requirements due to computer work
• Light to moderate lifting is required

J. Craig Venter Institute is an Equal Opportunity Employer. All qualified applicants are encouraged to apply and will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other legally protected characteristic or status.