Bioinformatics Programmer II

We are looking for a Bioinformatics Programmer! The Bioinformatics Programmer II works with limited supervision to formulate and define project scope and objectives through investigation and fact finding to develop or modify complex information systems handling biological data. He/she uses knowledge of molecular biology and computer science to manipulate and process complex data sets. Data management involves capturing information pertaining to biological and cellular activities captured using molecular biology methods, which may include microarray and next-generation sequencing.
ESSENTIAL DUTIES AND RESPONSIBILITIES
Responsibility A: Provides analysis for the design and modification of bioinformatics solutions.
• Analyzes and determines computerized solutions applicable for the services concerning compliance with regulatory agencies and the strategic plan or goals.
• Appraises effectiveness of systems flow, data usage, and manual or automated processes to identify ineffectiveness or inefficiency of the system(s)/programs(s).
• Develops, designs, and modifies technical specifications for bioinformatics applications.
• Coordinates the design and analysis of the implementation of new systems and the modifications of existing systems/programs.
• Works in close collaboration with TCH IS and Pathology Clinical Informatics teams for overlapping projects.
Responsibility B: Provides technical expertise in the implementation and modification of bioinformatics solutions.
• Provides technical support in determining solutions for the services concerning compliance with regulatory agencies and
the strategic plan or goals.
• Develops, designs, and modifies technical specifications for bioinformatics applications.
• Prepares detailed specifications and algorithms from which programs will be written.
• Investigates and assesses third-party bioinformatics software.
• Advises on hardware and software decisions related to efficient application of implemented software.
• Provides technical support in the design and analysis of the implementation of new systems and the modifications of
• existing systems.
• Act as a Change Control Lead to review and submit the reviewed change controls for final approval from appropriate
leadership to move changes into production.
Responsibility C: Implements and controls the configuration, development, and maintenance of bioinformatics
solutions.
• Controls system configuration and development process by establishing standards, measuring work in process, interpreting results, and taking corrective action.
• Develops and administers the system configuration and development plan.
• Delegates tasks and responsibilities to team members according to ability, priority, etc.
• Performs independent programming for segments of complex problems according to the technical specifications and
• standard system implementation techniques.
• Applies existing custom bioinformatics software to both well-defined and moderately-complex problems.
• Designs, codes, and maintains programs and investigates software for bioinformatics applications.
• Analyzes system performance and optimizes programs accordingly.
• Provides configuration, tuning, and upgrades to systems as needed.
• Imports, configures, and customizes third-party bioinformatics software.
• Initiates and implements new programming techniques, methods, procedures, approaches, and standards.
Responsibility D: Administers program and system tests.
• Develops and administers data verification methods and plans as needed.
• Tests and debugs programs and software for bioinformatics applications.
• Assures coded logic performs as required by testing and correcting programs via trial runs, and combines individual programs into a job stream.
• Performs system integration testing to ensure system integrity.
• Works in close collaboration with TCH IS and Pathology Clinical Informatics teams for overlapping projects.
Responsibility E: Develops system documentation.
• Develops documentation standards and regulatory requirements.
• Prepares program code documentation in compliance with standards and regulatory requirements.
• Prepares system configuration procedures in compliance with standards and regulatory requirements.
• Prepares documentation concerning program and configuration issues, bugs, and resolutions in compliance with standards and regulatory requirements
Responsibility F: Remains aware of any upcoming system enhancements.
• Works in close collaboration with TCH IS and Pathology Clinical Informatics colleagues to gain awareness of upcoming system upgrades and enhancements.
• Applies and conducts preliminary test on fixes and patches and reports pertinent information to the applicable leadership.
• Remains aware of and communicates to the Manager and Director(s) regarding upcoming system enhancements in a timely manner.
• Analyzes the impact, if any, on the department as well as the Hospital's operations, and reports to the applicable leadership in a timely manner of notice of enhancements as documented by the report.
• Provides training and education on enhancements to end-users.
Responsibility G: Prepares reports.
• Develops “ad hoc” reports as requested ensuring quality and thoroughness in providing analysis reporting to management by established deadline, as documented by reports.
• Assigns access to custom report through appropriate systems utilities, as needed.
• Assures proper daily, weekly, and monthly distribution, as needed to maintain efficiency in providing necessary and requested information to all department area.
Responsibility H: Troubleshoots and documents disruptions, providing a focal point for coordinating user and vendor support.
• Investigates and establishes solutions to problems arising out of daily production issues in collaboration with Medical Director(s), Assistant Director(s), TCH IS and Pathology Clinical Informatics colleagues.
• Coordinates issue resolution with the team.
• Works in close collaboration with TCH IS and Pathology Clinical Informatics teams for resolution of overlapping issues.
• Provide technical guidance and work direction to lower-level bioinformatics and information systems personnel.

Knowledge and Skills
• Experience with Python, databases and SQL
• Familiarity with the development cycle: build, debug, test, deploy, validate, document, maintain production-level software
• Familiarity with version control systems, continuous integration processes, reproducibility, data analysis and manipulation of data sets
• Working knowledge of object-oriented Python and familiarity with packages like biopython, pandas, numpy, scikit-learn and django
• Familiarity with web interfaces, bioinformatics databases, Illumina based NGS methods and tools
• Familiarity with variant detection in oncology
• Familiarity with other languages, e.g. R, C++, VBA
• Knowledge of current laboratory practices and computing systems, interfaces, and current standard software.
• Project management and planning, leadership skills, excellent written and verbal communication, analytical, and organizational skills, ability to analyze the functionality of systems and their fit with specifications, and the ability to work independently with minimum supervision.
• Key skills are observation, results oriented, and communication.
QUALIFICATIONS
Education
- Bachelor's Degree Biological science, Computer science, Computational/programming, or related technical area required
- Prefer master's degree Biological Science, Computational/Programming, Computer science, or related field
Experience
- 2 years Relevant bioinformatics experience in a clinical setting

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