DESCRIPTION

RESPONSIBILITIES

• Works with bioinformatics group members to develop functioning pipelines upstream of customized analysis workflows.
• Maintains pipelines by staying current with evolving algorithms and standards and incorporating into pipeline.
• Executes robust development testing for commonly used applications such as data processing pipelines.
• Optimizes performance of applications by working with scientific computing and information systems groups to optimize hardware/software parameters.
• Defines and prioritizes requirements for pipeline development over time to incorporate new technologies and platforms via functional communication with bioinformatics group members and bioinformatics end users.
• Identifies appropriate open-source and commercial products that serve needs of pipeline and/or customized analyses of end users.
• Implements and maintains commercial and open-source software for common bioinformatics and genomics data analysis.
• Implements, updates and maintains locally stored data resources required for various analysis tasks.
• Provides ad hoc support and one-on-one and group-based training on key bioinformatics software, features, and workflows.
• Provides efficient data management support including file transfers, data formatting and manipulation, and basic integration of data from a variety of experimental and reference resources.
• Develops and maintains working relationship with data providers such as sequencing cores within CHOP and infrastructure groups such as information systems.
• Continually keeps abreast of evolving data generation platform fundamentals, file-specific information representation, and strategic application of code base to optimize value of data.
• Maintains working knowledge of available commercial and openly accessible knowledge bases as they apply to bioinformatics analysis.

• Implements, maintains, and regularly contributes to formal and bioinformatics group-centralized code management system.
• Adopts appropriate forking and other strategies for robust code development. Apply to general bioinformatics group code base.
• Adopts 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.
• Ensures that all routinely used tools (e.g. those included in shared analysis pipelines) are versioned and managed through a source control system.
• Ensures that configuration files that provide parameters to algorithms and analysis software are versioned and managed through a source control system.
• Develops and implements automated data-driven testing processes that test reproducibility of results between versions of pipeline software.
• Develops and implements automated deployment processes that build and configure systems from source control repositories, eliminating the need to manually modify configuration files.
• Regularly documents code, troubleshoot, and provide training when necessary.

• Develops robust analysis plans under supervision.
• Incorporates QA/QC in analysis workflows.
• Delivers analytical endpoints such as feature identification, annotation, characterization, prioritization, etc.
• Reports results using, primarily, spreadsheets and, secondarily, abstracted materials such as slides and visuals.

• Attends group and team meetings and contributes primarily factual information regarding processes and approach.
• Defers to mentors and peers in establishing relationships, but works within boundaries to accomplish analytical goals.

REQUIREMENTS

PREFERENCES

• Strong UNIX/LINUX expertise required.
• Experience with Python, Perl, Scala, Ruby or other programming languages required.
• Experience with Apache Spark strongly preferred.
• Experience working under Zeppelin, Jupyter or other notebook environments strongly preferred.
• Experience with R strongly preferred.
• Experience with genomic data analysis strong 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 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.
• Eager to learn new things and contribute to scientific discoveries.

LOCATION

HOW TO APPLY

POLICY