Bioinformatics Engineer II

Posted on by Micaela Brun
Job ID: 15743
Job date: 2018-04-09
End Date:

Company : Children s Hospital of Philadelphia 

Country :

Role : Technician 


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Job Description:
The Center for Data-Driven Discovery in Biomedicine (D3b - d3b.center) is seeking talented bioinformatics engineers to build and scale solutions for accelerating discovery and advancements in child health. We’re 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 interactive bioinformatics application development. Successful candidates will gain deep knowledge about genomics sequencing data and its processing workflow. With this knowledge, this role will utilize Docker and CWL within the cloud computing environment like AWS and Google Cloud Platform to develop scalable systems and interactive applications that harmonize, analyze and visualize genomics data.

Job Responsibilities:

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: Bachelor’s 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: Master’s 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.

Requeriments :

Skills :

Areas :

Additional Info:
Shift: Days

Employment Status: AF - Active - Regular - Full Time

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