The Center for Data-Driven Discovery in Biomedicine (D3b - d3b.center) is seeking talented engineers to build and scale solutions for accelerating discovery and advancements in child health. Weíre looking for creative problem solvers who can leverage software and system engineering to perform large-scale genomic analysis. You will be involved in research projects that contain large cross-disease cohorts which are being characterized with next-generation sequencing. This role will have a strong focus on bioinformatics pipeline development, genomics data harmonization, as well as general data management, transferring and staging. Successful candidates will gain deep knowledge about important clinical and research phenotypes across a number of pediatric diseases. With this knowledge, this role will utilize controlled vocabularies, ontologies and associated methodologies to develop scalable systems that harmonize, store, and analyze these phenotypes in the context of genomics.
Specific responsibilities include:
Computational Development and Optimization (60%):
● Independently manage and develop large-scale bioinformatics pipelines
● Facilitate efficient transfer of bioinformatics data from data sources to data users with benchmarking and data quality checks
● Troubleshoot data quality issues or discrepancies
● Generally implement bioinformatics processing, storage, and manipulation of bioinformatics data in a cloud environment.
● Independently manage and evolve process for effectively using large-scale, cloud-based, bioinformatics storage frameworks
● Establish and implement integration and testing procedures following industry best practices for production bioinformatics systems integration and deployment
● Provide continuous assessment of commercial and open-source bioinformatics data resources and processing solutions
● Identify and test application/pipeline defects and fixes
● Work with technical team to establish and maintain appropriate levels of availability, response time, and performance of bioinformatics software and systems.
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
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. 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.
Required Education and Experience
Required Education: Bachelorís Degree in computational discipline or systems engineering
Required Experience: At least three (3) years of experience in a production clinical or research bioinformatics data processing role required.
Preferred Education, Experience & Cert/Lic
Preferred Education: Masterís degree in computational discipline or systems engineering
Preferred Experience: Four (4) years of experience or more in a production clinical or research bioinformatics data processing role.
Additional Technical Requirements
- Ability to independently plan and execute pipelines and workflows of high complexity required
- Knowledge of common NGS or other high-throughput data formats is required.
- Strong UNIX/LINUX expertise required
- Expertise in applications written in common bioinformatics languages such as Python, R, Perl or similar required
- Expertise in support mechanisms for common bioinformatics applications, data sources, and data formats required.
- Expertise with resources of genomic data sets and analysis tools, such as NCBI databases, UCSC Genome Browser, ENCODE, and others is required.
- Demonstrated ability to develop and implement best practices for bioinformatics systems integration, testing, and deployment is required.
- Ability to lead discussions with various information systems and technology owners to achieve desired bioinformatics outcomes is required.
- Knowledge with cloud computing concepts and applications is required.
All 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.
Children'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).
Children'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.
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