The Duke Center for Genomic and Computational Biology (GCB) is seeking a Genomics Data Manager and Programmer to administer, manage, and program the Laboratory Information Management System (LIMS), data management pipelines, and public data repository submission of various types of genomics data generated by research projects that heavily utilize next-generation sequencing and related technologies.
GCB was launched in July 2014 with the mission to foster innovative multi-disciplinary data-intensive research and education in the fields of genomic and computational biology. The Center employs state-of-the-art high-performance computing, networking, and storage infrastructure at a massive scale, and its faculty collaborates in teams that integrate approaches from different disciplines to solve complex problems not easily addressable within traditional departments.
The incumbent will initially work with at least two recently funded large genomics research projects, whose PIs are faculty at GCB. One, funded under the Genomics of Gene Regulation program of the NIH, aims to characterize how certain cells respond to anti-inflammatory drugs called glucocorticoids (a type of steroid hormone). The project will use next-generation sequencing (RNAseq and DNAseq) technologies to determine what and when genes are turned on and off, and how this process is controlled, which will advance the understanding of how glucocorticoids control both anti-inflammatory and metabolic responses. The second project, funded by NIH’s psychENCODE program, will use chromatin bases assays to identify active gene regulatory elements in brain tissue samples from 100 schizophrenia cases and controls. The research will use high-throughput reporter assays and genome editing technologies, which will generate unprecedented evidence for identifying and characterizing contributing genomic variants.
The incumbent will have three primary responsibilities.
- Customizing, programming, and administering the LIMS for genomic data. The LIMS is being implemented using CORE Informatics’ Core LIMS platform, which is cloud-based, provides a highly configurable user-interface, and a programmable API. The incumbent will manage the LIMS; use the Core LIMS infrastructure to implement new features, including tracking of new data types; and program report generation.
- Creating, programming and operating data management pipelines. The incumbent will develop best-practice protocols for storing, backup, and organization of genomics research data, and create pipelines that implement these practices, including standardized quality control pipelines for ensuring data integrity. The incumbent will also contribute to standardizing analysis pipelines.
- Automating high-quality data submission to public repositories. The incumbent will design, implement, and manage pipelines that retrieve metadata from the LIMS and automate the regular submission of well-documented and formatted data to pertinent public repositories, in particular NCBI’s Gene Expression Omnibus (GEO) and the database of ENCODE’s Data Coordinating Center (DCC). This will involve working with ENCODE DCC personnel to automate data submission.
The incumbent will report to Dr. Tim Reddy and will interact closely with GCB’s Informatics group.
- B.S. degree in a Bioinformatics, Computer Science, Information Technology, Information Science or related field.
- Programming skills in one or more scripting languages commonly used in scientific computing, most preferably Python.
- Strong experience working and programming in a Unix environment.
- Demonstrated ability to work independently.
Being effective in this position will also strongly benefit of the following skills and experience:
- Experience in working with and knowledge of relational databases.
- Programming REST-based APIs for querying, retrieving, and creating data records.
- Knowledge of best practices for with organizing, replicating, and backing up high-volume data.
- Experience with tracking and managing data and metadata in a LIMS.
- Familiarity with wrangling and analyzing genomics data, and applicable pipelines.
- Strong interpersonal and communication skills with a diversity of technical and non-technical collaborators.
Duke University is an Affirmative Action/Equal Opportunity Employer committed to providing employment opportunity without regard to an individual’s age, color, disability, genetic information, gender, gender identity, national origin, race, religion, sexual orientation, or veteran status.