Bioinformatics Engineer II - Rare Lung Disease Research Groups

Philadelphia, PA, US, 19104

​Location: LOC_ABRAMSON-Abramson Building 

Req ID: 220487

Shift: Days

Employment Status: Regular - Full Time 


Seeking Breakthrough Makers   

Children’s Hospital of Philadelphia (CHOP)—named America’s 2022 Best Large Employer by Forbes—offers countless ways to change lives. Our diverse community of more than 20,000 Breakthrough Makers will inspire you to pursue passions, develop expertise, and drive innovation.

At CHOP, your experience is valued; your voice is heard; and your contributions make a difference for patients and families. Join us as we build on our promise to advance pediatric care—and your career. 


CHOP’s Commitment to Diversity, Equity, and Inclusion 

CHOP is committed to building an inclusive culture where employees feel a sense of belonging, connection, and community within their workplace. We are a team dedicated to fostering an environment that allows for all to be their authentic selves. We are focused on attracting, cultivating, and retaining diverse talent who can help us deliver on our mission to be a world leader in the advancement of healthcare for children. 

We strongly encourage all candidates of diverse backgrounds and lived experiences to apply. 

Job Summary

This role is a 2nd stage position in a multi-lab pediatric rare lung disease research unit, for those with a moderate level of experience in the support of computational environments focused on the management and processing of complex data associated with genomics research studies.


The primary focus of this role is the development and maintenance of data analysis and visualization pipelines/applications on local enterprise compute resources for high throughput single-cell and bulk-RNA and DNA sequencing studies. Whereas the Bioinformatics Scientist is primarily focused on the outcome of an analysis in terms of the scientific endpoint, this role is primarily focused on the outcome of an analysis in terms of validity, robustness, and researcher accessibility. Implementing new software tools in Python and R, deploying nextflow/snakemake analysis pipelines to enterprise-managed cloud computing infrastructures using docker/kubernetes, and generating documentation to support long-term research unit goals are common tasks in this role.


The ideal candidate for this role has some experience in software engineering, bioinformatics pipeline development, and cloud computing infrastructures. The candidate will be primarily focused on supporting research groups and individuals as a software engineering and operational data management resource and will interface with institutional Research Information Services teams to accomplish tasks in this role. Activities occur with a moderate degree of supervision with moderate latitude for independent judgment.

Job Responsibilities

Computational Environment Development and Optimization (60%): 

  • Independently manage and evolve local large-scale bioinformatics pipelines.
  • Independently manage and evolve large-scale bioinformatics high performance computing (HPC) capability primarily at a local level. 
  • Independently manage and evolve process for effectively using enterprise-provided large-scale bioinformatics storage frameworks.
  • Work with IS and data center staff to ensure the appropriate installation, maintenance, and support of bioinformatics-dedicated hardware, software, and data storage.
  • Work with IS staff to establish and maintain appropriate levels of availability, response time, and performance of bioinformatics software and systems.
  • Establish and implement integration and testing procedures following industry best practices for production bioinformatics systems integration and deployment.
  • Facilitate efficient transfer of bioinformatics data from data sources to data users with benchmarking and data quality checks.
  • Operationally manage and evolve a robust heterogeneous UNIX, LINUX, OSX environment, including integration with enterprise resources.
  • Contribute to structured benchmark-based evaluation of new technologies.
  • Ensure the appropriate installation, maintenance, and support of bioinformatics-dedicated hardware, software, and data storage by collaborating with information systems and data coordination staff.
  • Implement bioinformatics processing, storage, and manipulation of bioinformatics data in a primarily local environment.
  • Engage with and participate in discussions related to endor-purchased systems and services usually under supervision.
  • Provide continuous assessment of commercial and open-source bioinformatics data processing solutions by applying structured benchmark evaluation.
  • Identify and test application/pipeline defects and fixes.
  • Troubleshoot data discrepancies.

Job Responsibilities (Continued)

Collaboration and Mentorship (20%):

  • Serve as engineering resource on a variety of bioinformatics-focused projects.
  • Serve as engineering facilitator by assessing all stakeholders, including bioinformatics management, bioinformatics scientists, information systems staff, and principal investigators  
  • Mentor lower tier engineering individuals and groups as needed
  • Advocate for developed solutions in discussions with external technology owners in order to ensure that enterprise systems allow for freedom of operation.

Documentation and Standardization (20%):

  • Under supervision, contribute to the development of a formal bioinformatics engineering plan and development roadmap.
  • Adopts and implements policies and standards for data quality, completeness, and reproducibility.
  • Adopts and implements policies and standards for performance benchmarking and system stability.
  • Maintain and audit all documentation required for transparency and reproducibility of operations and any relevant regulations (e.g., CAP, CLIA). Documentation may include configuration, processes, service records, asset inventories, topologies, admin manuals, job instructions, support contacts, and bug/issue tracking.
  • Install, maintain, and provide technical support for all software installations and associated hardware.

Required Education and Experience

Required Education: Bachelor’s Degree

Required Experience: Three (3) years of production, clinical or research bioinformatics data experience.

Preferred Education, Experience & Cert/Lic

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

Preferred Experience: Four (4) years of production, clinical or research bioinformatics data experience.

Additional Technical Requirements

  • Extensive knowledge with high performance and parallel computing environments and data processing workflows.
  • Extensive experience with data storage frameworks.
  • Extensive knowledge of CPU- and IO-intensive bioinformatics data analysis applications.
  • Demonstrated track record of optimizing systems to meet changing performance and load requirements.
  • 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.
  • Ability to independently plan and execute pipelines and workflows of high complexity.
  • Ability to independently engineer systems relative to larger enterprise framework.
  • Strong UNIX/LINUX expertise.
  • Expertise in support mechanisms for applications written in common bioinformatics languages such as R, Python, Perl or similar.
  • Expertise in support mechanisms for common bioinformatics applications, data sources, and data formats.
  • Knowledge of common microarray, NGS, mass spectrometry, or other high-throughput data formats.
  • Expertise with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases.
  • Demonstrated ability to develop and implement best practices for bioinformatics systems integration, testing, and deployment.
  • Expert knowledge with cloud computing concepts and applications.
  • Ability to lead discussions with various information systems and technology owners to achieve desired bioinformatics outcomes.

To carry out its mission, CHOP is committed to supporting the health of our patients, families, workforce, and global community.  As a condition of employment, professionals working onsite—at any CHOP location, for any portion of time—must be vaccinated for COVID-19. Learn more. 

CHOP also requires employees who work in patient care buildings to receive an annual influenza vaccine. Employees may request exemptions for valid religious and medical reasons.  Start dates may be delayed until candidates are immunized or exemption requests are reviewed.  

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