Bioinformatics Engineer II - The Genomic Diagnostic Laboratory

Philadelphia, PA, US, 19104

Location: LOC_ABRAMSON-Abramson Building 

Req ID: 137054

Shift: Days

Employment Status: Regular - Full Time 

Job Summary

The Genomic Diagnostic Laboratory (GDL) of the Children’s Hospital of Philadelphia is seeking Bioinformatics Engineer I with an interest in laboratory diagnostics to join our team. This is an exciting opportunity to work collaboratively within the bioinformatics team and together with our laboratory directors, supervisors, analysts, genetic counselors, and wet bench team to develop and improve pipelines and other tools to support accurate, timely diagnostic testing that has a direct impact on establishing the diagnosis, prognosis, treatment, and management plan for our patients. The team also supports cutting edge R&D efforts including new clinical test development and clinical research. The position is temporarily remote with the potential for long term remote flexibility. Seasoned professional and new graduate are welcome to apply and will be considered for the position commensurate with their experience.


The Bioinformatics Engineer II position is a 2nd stage position for those with a moderate level of experience in the support of computational environments focused on the management, transfer, formatting, and general processing of complex data types associated with genomics and proteomics. Whereas the Bioinformatics Scientist is primarily focused on the outcome of an analysis in terms of the scientific endpoint, the Bioinformatics Engineer is primarily focused on the outcome of an analysis in terms of validity, efficiency, and robustness. The focus of the position is implementation of data manipulation and analysis pipelines, applications, general hardware configurations, and bioinformatics-specific hardware configurations. The Bioinformatics Engineer II operates in a mostly local computing environment but may also is also represent the needs of largescale bioinformatics in strategic discussions where those local environments are mapped to enterprise solutions. The position allows for a wide variety of activities described within the job responsibilities and encompasses positions within both research and clinical environments. Activities occur with a moderate degree of supervision with moderate latitude for independent judgment. The Bioinformatics Engineer II will have some experience in best practices as a bioinformatics engineer resource. The Bioinformatics Engineer II is primarily focused on supporting bioinformatics analytical groups and individuals as an engineering domain resource and operational data resource. 


The Bioinformatics Engineer II must be able to perform all responsibilities listed in the Bioinformatics Engineer I job description. All responsibilities listed in this description are additional.                                                                                                                                                               

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.
    • Generally implement bioinformatics processing, storage, and manipulation of bioinformatics data in a primarily local environment.
    • Engage with and participate in discussions related to vendor-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.
  • 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 my 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.

Preferred Education, Experience & Cert/Lic

Preferred Education:

  • Master’s degree or Doctorate degree in computational discipline or systems engineering (e.g. computer science)


Preferred Experience: 

  • Previous experience with backend programming
  • Previous experience with full stack development
  • Previous experience with Ansible and deployment, server management
  • Previous experience working with human genetics data

Additional Technical Requirements

  • Proficient programming in python, Django, SQL and Postgres/MySQL
  • 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.
  • 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 required.
  • Ability to independently engineer systems relative to larger enterprise framework required.
  • Strong UNIX/LINUX expertise required.
  • Expertise in support mechanisms for applications written in common bioinformatics languages such as R, Python, Perl or similar required
  • Expertise in support mechanisms for common bioinformatics applications, data sources, and data formats required.
  • Knowledge of common microarray, NGS, mass spectrometry, or other high-throughput data formats is required.
  • Expertise with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases is required.
  • Demonstrated ability to develop and implement best practices for bioinformatics systems integration, testing, and deployment is required.
  • Expert knowledge with cloud computing concepts and applications is required.
  • Ability to lead discussions with various information systems and technology owners to achieve desired bioinformatics outcomes 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.

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.

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