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Bioinformatics Engineer I
Philadelphia, PA, US, 19104
Req ID: 26208
Employment Status: AF - Active
The Center for Data-Driven Discovery in Biomedicine (D3b, d3b.center) is seeking a talented engineer to build and scale workflow 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 pipeline, workflow development, and benchmarking of data from large cross-disease cohorts being characterized with next-generation sequencing.
The Bioinformatics Engineer I position is an entry-level position 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 basic systems implementation of data manipulation and analysis pipelines, applications, general hardware configurations, and bioinformatics-specific hardware configurations. Bioinformatics programming activities are also included. The Bioinformatics Engineer I primarily operates in a local environment as opposed to enterprise-level. The position allows for a wide variety of activities described within the job responsibilities and encompasses positions within both research and clinical environments. Activities occur with a high degree of supervision with low latitude for independent judgment. The Bioinformatics Engineer I will be introduced to the concepts of best practices in scripting, pipeline workflow development, hardware and software configurations, change controls, quality, sustainability, and documentation. The Bioinformatics Engineer I is primarily focused on supporting bioinformatics analytical groups and individuals as an engineering resource.
Computational Environment Development and Optimization (70%): Contribute to the maintenance and development of bioinformatics tool portfolio by developing knowledge of internally developed systems, open-source programs, and commercial applications. Provide efficient data management support.
Work with bioinformatics group members to develop functioning pipelines upstream of customized analysis workflows.
Maintain pipelines by staying current with evolving algorithms and standards and incorporating into pipeline
Optimize performance of applications by working with scientific computing and information systems groups to optimize hardware/software parameters
Define and prioritize requirements for pipeline development over time to incorporate new technologies and platforms via functional communication with bioinformatics group members and bioinformatics end users
Identify appropriate open-source and commercial products that serve needs of pipeline and/or customized analyses of end users.
Implement and maintain commercial and open-source software for common bioinformatics and genomics data analysis.
Implement, update and maintain locally stored data resources required for various analysis tasks.
Provide efficient data management support including file transfers, data formatting and manipulation, and basic integration of data from a variety of experimental and reference resources.
Maintain working knowledge of available commercial and openly accessible knowledgebase as they apply to bioinformatics analysis.
Collaboration and Mentorship (10%)
Collaborate primarily with bioinformatics scientist group and equivalents to produce local scale computational environments
Works with both bioinformatics group members and end users/clients to understand specific needs in bioinformatics and end user-specific domains
Attends group and team meetings and contributes primarily factual information regarding processes and approach
Provide ad hoc support and one-on-one and group-based training on key bioinformatics software, features, and workflows
Documentation and Standardization (20%):
Documents all aspects of computational environment parameters, instructions, and SOP's for existing systems and newly implemented systems.
Ensure that all routinely used tools (e.g. those included in shared analysis pipelines) are versioned and managed through a source control system.
Ensure that configuration files that provide parameters to algorithms and analysis software are versioned and managed through a source control system
Required Education and Experience
Required Education: Bachelor's Degree in biological or computational discipline
Preferred Education, Experience & Cert/Lic
Preferred Education: Master's Degree in biological or computational discipline
Preferred Experience: Previous experience in applied bioinformatics, computational, and genomics/proteomics areas
Additional Technical Requirements
Strong UNIX/LINUX expertise required.
Experience with R strongly preferred
Experience with Python, Perl, or other languages preferred.
Experience with pipeline or workflow development frameworks preferred.
Experience with data management preferred.
Familiarity with open source and commercial bioinformatics resources and software preferred.
Experience with genomic data analysis preferred.
Experience or knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture preferred.
Knowledge of the working mechanism of microarray, NGS, mass spectrometry, or other high-throughput technologies and awareness of their strengths and weaknesses, as well as applicability to a specific biological problem is preferred.
Familiarity with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases is preferred.
Accountability and attention to timelines.
Excellent organization and communication skills with an emphasis on strong presentation skills
Ability to work in a team environment.
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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