Bioinformatics Engineer

SHIFT:

Any (United States of America)

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CHOP 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 Overview
NOTICE - This job is an hourly version of our existing salaried role. This version of the job should only be used for employees below the government-mandated, minimum FLSA pay threshold. All other employees should be placed in the salaried version of this role.
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.
What you will do

• 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
• Execute robust development testing for commonly used applications such as data processing pipelines
• 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.
• Develop and maintain working relationship with data providers such as sequencing cores within CHOP and infrastructure groups such as information systems.
• Continually keep abreast of evolving data generation platform fundamentals, file-specific information representation, and strategic application of code base to optimize value of data.
• Maintain working knowledge of available commercial and openly accessible knowledge bases as they apply to bioinformatics analysis.
• Implement, maintain, and regularly contribute to formal and bioinformatics group-centralized code management system.
• Adopt appropriate forking and other strategies for robust code development. Apply to general bioinformatics group code base.
• 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
• Adopt best practices for code development consistent with larger bioinformatics group. This includes choice of language based on the type of solution being developed, the likely life cycle and downstream usage of the resulting application, and integration with other systems.
• Develop and implement automated data-driven testing processes that test reproducibility of results between versions of pipeline software.
• Develop and implement automated deployment processes that build and configure systems from source control repositories, eliminating the need to manually modify configuration files
• Regularly document code, troubleshoot, and provide training when necessary

Education Qualifications

• Bachelor's Degree Required
• Master's Degree biological or computational discipline Preferred

Experience Qualifications

• Previous experience in applied bioinformatics, computational, and genomics/proteomics areas Preferred

Skills and Abilities

• Strong UNIX/LINUX expertise required. (Required proficiency)
• Experience with R strongly preferred. (Preferred proficiency)
• Experience with Python, Perl, or other languages preferred. (Preferred proficiency)
• Experience with pipeline or workflow development frameworks preferred. (Preferred proficiency)
• Experience with data management preferred. (Preferred proficiency)
• Familiarity with open source and commercial bioinformatics resources and software preferred. (Preferred proficiency)
• Experience with genomic data analysis preferred. (Preferred proficiency)
• Experience or knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture preferred. (Preferred proficiency)
• 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. (Preferred proficiency)
• Familiarity with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases is preferred. (Preferred proficiency)
• Accountability and attention to timelines. (Required proficiency)
• Excellent organization and communication skills with an emphasis on strong presentation skills. (Required proficiency)
• Ability to work in a team environment. (Required proficiency)

To carry out its mission, CHOP is committed to supporting the health of our patients, families, workforce, and global community. As a condition of employment, CHOP employees who work in patient care buildings or who have patient facing responsibilities must be fully vaccinated against COVID-19 and receive an annual influenza vaccine. Learn more.
Employees may request exemptions for valid religious and medical reasons. Start dates may be delayed until candidates are immunized or exemption requests are reviewed.
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