Children's Hospital of Philadelphia · 1 day ago
Software Engineer II: Genomic Medicine and Diagnostics
Philadelphia, PA
Full-time
Hybrid
Mid, Senior Level
$99K/yr - $126K/yr
3+ years expChildren’s Hospital of Philadelphia (CHOP) is seeking a highly motivated Software Engineer II to join their Genomic Diagnostic Laboratory team. The role involves developing and optimizing bioinformatics pipelines and tools to support accurate diagnostic testing, while collaborating with various teams to enhance laboratory diagnostics.
Non ProfitFamily & CareHealthcareHospitalChild CareHealth CareMedical
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
Qualification
Required
Bachelor's Degree - Required
At least three (3) years production, clinical or research bioinformatics data experience - Required
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
Preferred
Master's Degree computational discipline or systems engineering - Preferred
At least four (4) years production, clinical or research bioinformatics data experience - 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)
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
Company
Children's Hospital of Philadelphia
Since its start in 1855 as the nation's first hospital devoted exclusively to caring for children, The Children's Hospital of Philadelphia has been the birthplace for many dramatic firsts in pediatric medicine.
10001+ employees
H1B Sponsorship
Children's Hospital of Philadelphia has a track record of offering H1B sponsorships. Please note that this does not
guarantee sponsorship for this specific role. Below presents additional info for your
reference. (Data Powered by US Department of Labor)
Distribution of Different Job Fields Receiving Sponsorship
Represents job field similar to this job
Trends of Total Sponsorships
2025 (175)
2024 (170)
2023 (140)
2022 (115)
2021 (70)
2020 (53)
Funding
Current Stage
Late StageTotal Funding
$33.35MKey Investors
UnitedHealthcare Community PlanNational Cancer InstituteBill & Melinda Gates Foundation
2025-12-10Grant· $1.7M
2025-09-29Grant· $1M
2025-06-18Grant· $1M
Leadership Team
Adam Resnick
Director of the Center for Data Driven Discovery in Biomedicine (D3b)
Benjamin Laskin
Chief of Nephrology
Recent News
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