Software Engineer II: Genomic Medicine and Diagnostics

Children's Hospital of Philadelphia; Philadelphia (Philadelphia County); Hybrid; USD 101,000 - 129,000; Full time

Job summary

Children’s Hospital of Philadelphia (CHOP) is seeking a Software Engineer II to join the Genomic Diagnostic Laboratory's bioinformatics team. You will help develop and optimize pipelines and tools that support diagnostic testing and research while collaborating with lab directors, analysts and D&T services.

The role emphasizes Python development, HPC, UNIX/Linux environments, and data workflows, with opportunities to work on ETL, APIs, and cloud concepts.

Qualifications

• Bachelor's degree required in a computational discipline or related field.
• 3+ years in production, clinical or research bioinformatics data experience.
• 4+ years experience preferred in bioinformatics data processing.
• Extensive knowledge of high performance/parallel computing environments.
• Experience with HPC systems, job management and benchmarking.

Responsibilities

• Develop and optimize local large-scale bioinformatics pipelines.
• Manage HPC capability and data storage with IT and data center staff.
• Ensure availability and performance of bioinformatics software.
• Collaborate across stakeholders including lab management and D&T staff.
• Lead testing, deployment, and documentation of pipelines and tools.

Skills

Python development

Git

Unix/Linux

SQL

Full stack development

Ansible

HPC and job management (Slurm/qsub)

APIs (REST/GraphQL)

Workflow tools (Nextflow/Snakemake/CWL

RHEL OS

Education

Bachelor's Degree

Master's Degree in computational discipline or systems engineering

Tools

Git

Nextflow

Snakemake

CWL

WDL

REST API

GraphQL

Ansible

qsub/Slurm

Job description

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.

SHIFT:
Day (United States of America)

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 does not discriminate on the basis of race, color, sex, national origin, religion, or any other legally protected categories in any employment, training, or vendor decisions or programs. CHOP recognizes the critical importance of a workforce rich in varied backgrounds and experiences and engages in ongoing efforts to achieve that through equally varied and non-discriminatory means.

A Brief Overview

The Genomic Diagnostic Laboratory (GDL) of the Children’s Hospital of Philadelphia is seeking a highly motivated Software Engineer II 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 ability to communicate in a highly matrixed environment will be key to the candidate’s success. Seasoned professionals as well as new graduates are welcome to apply and will be considered for the career ladder position commensurate with their experience. This position is hybrid with weekly onsite work at our Philadelphia campus as appropriate.

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
• Full stack development
• Ansible and deployment, server management
• Backend programming (devops)

In addition, experience in some of the following is preferred:

• Developing ETL 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 Nextflow, Snakemake, CWL or WDL)

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 data center staff to ensure the appropriate installation, maintenance, and support of bioinformatics-dedicated hardware, software, and data storage.
• Work with IT 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 Digital & Technology Services 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, Digital & Technology Services 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, 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

Skills And Abilities

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

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 receive an annual influenza vaccine.

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SALARY RANGE

$101,300.00 - $129,100.00 Annually
Salary ranges are shown for full-time jobs. If you're working part-time, your pay will be adjusted accordingly.
At CHOP, we are committed to fair and transparent pay practices. Factors such as skills and experience could result in an offer above the salary range noted in this job posting.