Software Engineer II: Genomic Medicine and Diagnostics

Children's Hospital of Philadelphia • Philadelphia, PA

2d • $98,820 - $126,000 • Hybrid

About The Position

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.

Requirements

• 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)
• Bachelor's Degree
• At least three (3) years production, clinical or research bioinformatics data experience
• 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/GNU-LINUX expertise.
• Expertise in support mechanisms for applications written in common bioinformatics languages such as R, Python, Perl or similar.
• 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

Nice To Haves

• 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)
• Master's Degree computational discipline or systems engineering
• At least four (4) years production, clinical or research bioinformatics data experience
• 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

Responsibilities

• 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.
• 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.
• 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.

Benefits

• 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 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.
• 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.
• Click here for more information regarding CHOP's Compensation and Benefits.

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level