Bioinformatician A

Job Description Summary

The Kaestner Lab (Dept. of Genetics, University of Pennsylvania) is seeking a meticulous and technically skilled Bioinformatician to oversee the organization, storage, retrieval, and long-term preservation of large-scale bioinformatics datasets. This position ensures that genomic, transcriptomic (bulk, single cell, spatial), and other high-throughput biological data (including images) are securely managed, efficiently stored and retrieved, and cost-effectively archived-supporting the University's mission of open, reproducible, and sustainable data-driven research.

Job Responsibilities

• Data Organization: Design, implement, and maintain structured file systems, standardized naming conventions, and metadata schemas for bioinformatics data (e.g., NGS, imaging). This includes managing our in-house database for record keeping.
• Access & Security: Manage access permissions, version control, and audit trails across HPC, local servers, tape, and cloud platforms.
• Cloud & Archival Storage: Administer tape- and cloud-based storage environments (AWS S3, Dropbox, Box, institutional repositories) and coordinate archival and retrieval strategies.
• Cost Monitoring & Optimization: Track and analyze storage utilization and expenses across on-premises, tape, and cloud systems; develop policies to optimize resource allocation and reduce costs.
• Data Integrity & Backup: Ensure redundancy, perform integrity checks, and manage automated backup processes.
• Data Transfers: Perform secure data transfers to and from public repositories (such as dbGaP, SRA) following institutional and funding agency's mandated policies.
• Documentation & Training: Maintain comprehensive documentation of file structures, workflows, and storage protocols; train researchers on best practices for data management and archival.
• Collaboration: Work closely with IT, research computing teams, and PIs to align storage strategies with project and compliance requirements (e.g., NIH, NSF).
• Preprocessing Pipelines: Execute predefined preprocessing or quality control pipelines (e.g., FASTQ QC, format conversion, alignment) on high-throughput datasets using HPC or cloud workflows.
• Other duties and responsibilities as assigned

Qualifications

• Bachelor of Science and 3 to 4 years of experience or equivalent combination of education and experience is required.

Position is contingent upon continued funding.