Bioinformatics Software Engineer III

Philadelphia, PA, US, 19146

Job Type: 

ROBERTS - Roberts Ctr Pediatric Research Req ID: 27804

Shift: Days

Employment Status: AF - Active - Regular - Full Time 

Job Summary

The Children’s Hospital of Philadelphia (CHOP) Research Institute and its Dept of Biomedical and Health Informatics (DBHi) are seeking a software engineer to help build an enterprise-level data and informatics platform called “Arcus”. The Arcus team integrates with major scientific initiatives in the Research Institute strategic plan, high-impact research areas such as lifespan, rare diseases, novel devices and therapeutics, and precision health.


This role will work with a team of bioinformatics scientists, software engineers and genomics faculty focused on architecting and implementing a cloud-native platform to support storing and analyzing enterprise wide genomic data including data management, harmonized pipelines, and variant warehouse components. We are looking for highly creative people who share our mission to advance child health and who will thrive in a continuous learning environment, acquiring and applying both new technical skills and biomedical domain knowledge.

Job Responsibilities

o    Evaluate trends in bioinformatics data production and analysis and identify requirements for bioinformatics data processing and storage systems.
o    Monitor new bioinformatics technologies, assess relevance to research or clinical systems, and contribute to benchmarking and evaluation.
o    Implement current best practices for bioinformatics processing, storage, and manipulation of bioinformatics data.
o    Use of and integration with cloud services offered by Google Cloud Platform.
o    Communicate solutions to stakeholders, including bioinformatics management, bioinformatics scientists, information systems staff, and principal investigators
o    Lead the development of a formal bioinformatics engineering plan and development roadmap.
o    Contribute to the design and implementation of service APIs exposing bioinformatics capabilities.
o    Establish policies and standards for data quality, completeness, and reproducibility.
o    Establish policies and standards for performance benchmarking and system stability.
o    Leads preparation and successful response program for audit and adherence to applicable regulatory requirements (e.g., HIPAA, CAP, CLIA).
o    Promote sustainability and enterprise adoption through proactive documentation.

Required Education and Experience

Required Education: Bachelor’s Degree in computational discipline or systems engineering

Required Experience: At least seven (7) years of experience in a production clinical or research bioinformatics data processing role.

Preferred Education, Experience & Cert/Lic


Preferred Education: Master’s degree in computational discipline or systems engineering

Preferred Experience: Eight (8) years of experience or more in a production clinical or research bioinformatics data processing role.

Additional Technical Requirements

•    Extensive knowledge with high performance and parallel computing environments and data processing workflows essential.
•    Extensive experience with data storage frameworks essential.
•    Extensive knowledge of CPU- and IO-intensive bioinformatics data analysis applications.
•    Extensive knowledge of HPC systems, job management applications, including methods for profiling performance, benchmarking, and optimizing multiple job types and scenarios in bioinformatics data processing.
•    Knowledge of Next Generation Sequencing (NGS) or other high-throughput data formats is required.
•    Expertise in support mechanisms for applications written in common bioinformatics languages such as R, Python, Perl or similar required
•    Expertise with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases is required.
•    Demonstrated track record of optimizing systems to meet changing performance and load requirements.
•    Familiarity with service API design over HTTP or gRPC.
•    Experience with Go is desired.
•    Experience with Python is required.

All CHOP employees who work in a patient building or who provide patient care are required to receive an annual influenza vaccine unless they are granted a medical or religious exemption.

Children's Hospital of Philadelphia is committed to providing a safe and healthy environment for its patients, family members, visitors and employees. In an effort to achieve this goal, employment at Children's Hospital of Philadelphia, other than for positions with regularly scheduled hours in New Jersey, is contingent upon an attestation that the job applicant does not use tobacco products or nicotine in any form and a negative nicotine screen (the latter occurs after a job offer).

Children's Hospital of Philadelphia is an equal opportunity employer. We do not discriminate on the basis of race, color, gender, gender identity, sexual orientation, age, religion, national or ethnic origin, disability or protected veteran status.

VEVRAA Federal Contractor/Seeking priority referrals for protected veterans.  Please contact our hiring official with any referrals or questions.

CHOP Careers Contact 

Talent Acquisition

2716 South Street, 6th Floor

Philadelphia, PA 19146 

Phone: 866-820-9288




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