Reference #: 1008105
SHIFT:Day (United States of America)Seeking Breakthrough MakersChildren'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 InclusionCHOP 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 OverviewThe 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 idealcandidate 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 SQLAn 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 encompas es 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 r