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Seeking Breakthrough Makers

Children's Hospital of Philadelphia (CHOP) 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.

A Brief Overview

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 ideal candidate will have experience in the following:

Software development in Python (including working with Git and writing unit tests)
BASH scripting/Unix command line
Reading and comprehending SQL

An ideal candidate will have experience in some of the following:

Developing ETL (Extract/Transform/Load) workflows between SQL databases
Deploying and troubleshooting of Virtual Machines (specifically ones running RHEL OS)
Developing and/or utilizing APIs (either REST-ful or GraphQL-based)
Submission + troubleshooting of HPC jobs via scheduler (slurm, qsub, etc)
Use of open-source tools for processing NGS data (preferably in a reproducible manner via a workflow language such as Snakemake or WDL)
Backend programming (devops)
Full stack development
Ansible and deployment, server management
Human genetics data (next generation sequencing data)

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.

What you will do

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.
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.

Education Qualifications

Bachelor's Degree Required
Master's Degree computational discipline or systems engineering Preferred

Experience Qualifications

At least three (3) years production, clinical or research bioinformatics data experience. Required
At least four (4) years production, clinical or research bioinformatics data experience Preferred

Preferred Experience:

Four (4) or more years of experience in a production clinical or research bioinformatics data processing role
Experience with backend programming (devops) is preferred
Experience with full stack development is preferred
Experience with Ansible and deployment, server management is preferred
Experience working with human genetics data is preferred

Skills and Abilities

Proficient programming in python, Django, SQL and Postgres/MySQL is required.
Strong UNIX/LINUX expertise required
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
Knowledge and experience with WDL, airflow, buildbot and JavaScript is a plus.
Ability to independently engineer systems relative to larger enterprise framework 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.

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, CHOP employees who work in patient care buildings or who have patient facing responsibilities must be fully vaccinated against COVID-19 and receive an annual influenza vaccine. Learn more.

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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