Biomedical Informatics Data Specialist

Institution/Company:
Medical Science and Computing (a Guidehouse Company)
Location:
Rockville, Maryland, United States
Job Type:
  • Programmer/Developer
Degree Level Required:
Bachelor's
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Biomedical Informatics Data Specialist

  • 3+ years of Python and Bash scripting
  • Writing Snakemake or similar pipelines
  • HPC computing
  • Contribute code with team members using git
  • Bioinformatics
  • Human Clinical Genomics
  • OMIM, Gnomad, ClinVar, HGMD, and other databases
  • Handling and exploring VCF files
  • High level communication, documentation, organizational, and time-management skills

Responsibilities:

  • Work closely with a small diverse team of scientists and engineers to deliver high-quality data
  • Document and design data models
  • Extract, integrate, and reconcile new data sources with existing knowledge bases
  • Perform quality control on data to ensure that it meets requirements
  • Working with the project team and an enterprise infrastructure team to test the impact of new functionality on data
  • Experiment with new data management technologies and systems and prototyping solution
  • Working within the developer team to share knowledge, collaboratively developing best practices
  • Working with Stakeholders, Users, and Project Managers to meet NIH Project Goals and Milestones

Qualifications:

  • BS. or higher degree in computational life sciences or related field.
  • Demonstrated expert fluency (3+ years working experience) in using Python for bioinformatics or biomedical informatics data management pipelines
  • Experience with snakemake pipelines
  • Proficiency in the use of UNIX/Linux and bash scripting
  • Experience with high performance computing and cloud environments
  • Experience with common clinical genomic file formats (primarily VCF, but also BAM)
  • Experience using Git and GitHub for tracking code changes and sharing contributions of multiple team members
  • Demonstrated experience extending the functionality of existing software; ability to learn an existing body of code and extend it.
  • Experience with annotating human genomes with annotations through scripting and the use of reference genome databases
  • Knowledge of public genomic databases such as OMIM, Gnomad, ClinVar, HGMD, others
  • Excellent communication skills and ability to work with users, including to develop and document requirements
  • Excellent organizational and time-management skills
  • Experience communicating with end users on software development projects

Secondary Qualifications:

  • Experience mapping reads to human genome reference databases and understanding of challenges in migrating annotations between genome reference versions (GRCH.37 / GRCH.38)
  • Experience reviewing mapped reads using genome browsers such as IGV
  • Experience working with human genome variant calling pipelines such as GATK
  • Solid understanding of human genome annotation databases (gnomAD, 1000 genome, ExAC)
  • Demonstrated knowledge of scientific data sources, data structures, and mapping data to models
  • Demonstrated skills in extracting, integrating, and reconciling new data sources with existing knowledge bases

Bonus Qualifications:

  • Experience with CLIA compliant clinical genomics pipelines
  • Experience with the product LabKey
  • Experience with developing data visualizations and dashboards
  • Familiarity with relational and non-relational database systems (SQL, MongoDB, Neo4j)
  • How to Apply

    To apply please email your CV or resume.