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Black Canyon ConsultingBlack Canyon ConsultingBethesda, MD

Data Engineer

Develops and maintains software for NCBI's biomedical databases like PubMed and GenBank, implementing bioinformatic algorithms and cloud pipelines for large-scale genetic data. Requires Python proficiency, SQL expertise, Linux scripting, and experience with big data handling.

Salary not listed
On-siteData Engineering

About the role

Responsibilities

  • Design, develop, test, and maintain programs for NCBI's biomedical data resources (PubMed, GenBank, SRA, ClinicalTrials.gov).
  • Implement efficient bioinformatic algorithms.
  • Develop cloud-ready tools and pipelines to improve performance and scalability for searching and submitting genetic sequence data.

Required Skills

  • Proficiency in Python
  • Experience with MS SQL Server and relational database design/optimization
  • Programming in Linux environment and BASH shell scripts
  • Handling large amounts of data
  • Working with structured documents (XML, JSON)
  • CI/CD pipelines, unit/integration/regression testing

Desired Skills

  • Cloud technologies: AWS (EC2, S3, Lambda), GCP (GKE, Google Storage, Cloud Functions)
  • 5+ years with genetic/biological data
  • NGS tools/formats (BWA, GATK, Galaxy)
  • Open source involvement (GitHub)
  • Managing production workflows for online public databases
  • RESTful API design

Skills

PythonMs Sql ServerLinuxBashXmlJSONCI/CDAWSGCPNgsBwaGatkGalaxyREST APIsGitHub
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