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Bioinformatics Engineer II

Company name
Cielo, Inc.

Location
Philadelphia, PA

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Job Description
Req ID: 14321\r\rShift: Days\r\rEmployment Status: AF - Active - Regular - Full Time \r\r\rJob Summary\r\r
\rThe Children’s Hospital of Philadelphia (CHOP) Research Institute is recruiting a Bioinformatics Engineer II in the Data Coordination and Analysis Team (DCAT) of the Bioinformatics Group in the Department of Biomedical and Health Informatics.  This individual will support the management and analysis of genomic and phenotypic data within the CHOP Roberts Collaborative, which is at the forefront of pediatric genetics research and takes a multidisciplinary approach toward diagnostics, clinical management, consulting, therapeutics and research driven by the power of genetics. The successful candidate will have a pivotal role in helping to decode drivers of rare disease in children.\r\r\r \rAbout DCAT: The DCAT team is looking to hire mission-driven professionals with experience in large-scale genomic and phenotypic data management, integration and analysis. Members of the team are involved in data processing and analysis locally and on the cloud to serve both internal and external large-scale projects using next-generation sequencing technologies. Team members are involved in highly visible research projects with large cross-disease and cross-institutional cohorts. Successful candidates will gain deep knowledge about important clinical and research phenotypes across a number of pediatric diseases. Members of the DCAT team work with stakeholders in large bioinformatics-driven projects and our Scientific Computing team to deliver analyzed results and data management solutions that can lead to publications and academic visibility connected to their work.\r\rJob Responsibilities\r\r
\rJob Responsibilities:\r\r\r• Computational Environment Development and Optimization:\r\r\ro Integrate large-scale bioinformatics pipelines into larger sustainable enterprise data processing solutions.\ro Integrate large-scale bioinformatics high performance computing (HPC) capability into larger sustainable enterprise analytical solutions.\ro Integrate large-scale bioinformatics storage frameworks into larger sustainable enterprise storage solutions.\ro Lead the development and evolution of a robust heterogeneous UNIX, LINUX, OSX environment.\ro Evaluate trends in bioinformatics data production and analysis and identify likely requirements for bioinformatics data processing and storage systems. Communicate value of trends/innovations to organization using metrics and forecasting.\ro Implement best practices for bioinformatics processing, storage, and manipulation, and archiving of bioinformatics data\ro Assist in modeling, development, and testing of databases (SQL / NoSQL)\ro Implements programs for continuous assessment of commercial and open-source bioinformatics data processing solutions by applying structured benchmark evaluations.\r\r\r• Assists in projects where needed by serving as engineering point, especially for solutions involving coordination of multiple disciplines.\r\r\r• Documentation and Standardization:\r\r\ro Under supervision, lead the development of a formal bioinformatics engineering plan and development roadmap.\ro Supports policies and standards for data quality, completeness, and reproducibility.\ro Supports policies and standards for performance benchmarking and system stability.\ro Supports the execution of a robust data quality program, focused on transparency and reproducibility of results.\ro Promotes sustainability and enterprise adoption through proactive documentation.\r \r\rRequired Education and Experience\r\r
\r• BS/MS in computational discipline required. BS/MS in systems engineering is preferred.\r• 3-10 years experience in a production clinical or research bioinformatics data processing role required.\r• Extensive knowledge with high performance and parallel computing environments and data processing workflows essential.\r• Extensive experience with data storage frameworks essential.\r• Extensive knowledge of CPU- and IO-intensive bioinformatics data analysis applications.\r• Demonstrated track record of optimizing systems to meet changing performance and load requirements.\r• 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.\r• Ability to independently plan and execute pipelines and workflows of high complexity required.\r• Ability to independently engineer systems relative to larger enterprise framework required.\r• Strong UNIX/LINUX expertise required.\r• Experience in version control management in tools such as Git required.\r• Expertise in support mechanisms for applications written in common bioinformatics languages such as R, Python, Perl or similar required\r• Expertise in support mechanisms for common bioinformatics applications, data sources, and data formats required.\r• Knowledge of common microarray, NGS, mass spectrometry, or other high-throughput data formats is required.\r• Expertise with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases is required.\r• Demonstrated ability to develop and implement best practices for bioinformatics systems integration, testing, and automated deployment is required.\r• Expert knowledge with cloud computing concepts and applications is required.\r• Ability to lead discussions with various information systems and technology owners to achieve desired bioinformatics outcomes is required.\r \r\rAll CHOP employees who work in a patient building or who provide patient care are required to receive an annual influenza vaccine unless they are granted a medical or religious exemption.\r\rChildren's Hospital of Philadelphia is committed to providing a safe and healthy environment for its patients, family members, visitors and employees. In an effort to achieve this goal, employment at Children's Hospital of Philadelphia, other than for positions with regularly scheduled hours in New Jersey, is contingent upon an attestation that the job applicant does not use tobacco products or nicotine in any form and a negative nicotine screen (the latter occurs after a job offer).\r\rChildren's Hospital of Philadelphia is an equal opportunity employer. We do not discriminate on the basis of race, color, gender, gender identity, sexual orientation, age, religion, national or ethnic origin, disability or protected veteran status.\r\rVEVRAA Federal Contractor/Seeking priority referrals for protected veterans.  Please contact our hiring official with any referrals or questions.\r\rCHOP Careers Contact \r\rTalent Acquisition\r\r2716 South Street, 6th Floor\r\rPhiladelphia, PA 19146 \r\rPhone: 866-820-9288 \r\rEmail:TalentAcquisition@email.chop.edu\r\r\r\r

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Cielo, Inc.

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