Bioinformatics DevOps Engineer/Developer

1 week ago

Jacksonville, Florida, United States WiredPeople, Inc. Full time

Overview:

WiredPeople is seeking to hire a Bioinformatics DevOps Engineer/Developer - Advanced Molecular Detection to help support genomic surveillance and outbreak investigations for pathogens of public health concern in Florida.

The Bioinformatics DevOps Engineer/Developer will work directly with the Bioinformatics Team, serving as a bioinformatics developer and primarily support the development and implementation of a cloud computing architecture to improve and expand our current computational infrastructure.

Responsibilities:

  • Plan and execute whole-genome sequencing analysis, comparative genomic analysis, and other analytic research projects, establishing new standard operating procedures (SOPs) by developing custom bioinformatics pipelines/workflows.
  • Select and develop appropriate analysis techniques and measures and identify and implement the necessary software and databases to complete defined analytical tasks.
  • Develop, manage, and curate databases for analysis.
  • Identify, implement, and maintain data quality control, data submissions and management programs.
  • Lead the development and implementation of a cloud computing architecture to improve and expand our current computational infrastructure.
  • Provide telephonic and web based technical assistance to other bioinformaticians, laboratory staff, and epidemiologists on the use of complex data analysis techniques and methods.
  • Provide approved updates with analytical results from developed bioinformatic pipelines to be disseminated to laboratory and epidemiological staff.
  • Lead and coordinate with other bioinformaticians involved in analysis projects, including data sharing and engagement across multidisciplinary project teams.
  • Disseminate approved results of research projects in a wide range of venues including publications, peer reviewed journals, summaries, manuscripts, special reports, and oral/poster presentations.
  • Attend approved training workshops and complete a corresponding report on the training received.

Qualifications and Experience:

Required:

  • A PhD in bioinformatics, genomic epidemiology, microbiology, virology, parasitology, evolutionary biology, microbial genetics, molecular biology, computer science, or related field.
  • At least five years of practical and technical experience in microbial and/or public health bioinformatics.
  • At least five years of experience with bioinformatic development of pipelines for the phylogenetic and comparative genomic analysis of microbial organisms.
  • At least two years of experience with cloud computing.
  • Bioinformatics experience with microbiology and/or public health applications.
  • Experience working in a UNIX/LINUX environment and writing shell scripts.
  • Proficiency in at least one scripting/programming language (e.g., Python, Perl, R, C++, Java) and willingness to learn new languages, if necessary.
  • Experience developing custom scripts and executing command-line bioinformatics tools for microbial genomics comparative analysis (i.e., assembly, annotation, variant detection, multiple sequence alignment, phylogenetic tree building, pairwise SNP matrices, etc.).
  • Experience in phylogenetics and interpreting comparative genomic data from microbial organisms.
  • Experience using git/github.
  • Experience querying and submitting genomic data from/to NCBI databases.
  • Excellent verbal communication with experience presenting complex, technical data to multidisciplinary teams.
  • Excellent written communication and experience publishing in the relevant scientific literature.

Preferred:

  • Strong background in phylogenetics of bacterial and/or viral pathogens.
  • Proficiency in Python and R.
  • Experience analyzing NGS data generated from Illumina, Oxford Nanopore, and PacBio platforms.
  • Experience with high-performance computing (HPC) and/or cloud computing.
  • Experience with Singularity and/or Docker.
  • Experience with Conda.
  • Experience developing and/or executing workflows using a workflow language (such as Snakemake, Nextflow, WDL).
  • Experience with pathogen genomics, especially of public health concern.

WiredPeople provides equal employment opportunities (EEO) to all employees and applicants for employment without regard to race, color, religion, sex, national origin, age, disability, or genetics. In addition to federal law requirements, WiredPeople complies with applicable state and local laws governing nondiscrimination in employment in every location in which the company has facilities. This policy applies to all terms and conditions of employment, including recruiting, hiring, placement, promotion, termination, layoff, recall, transfer, leaves of absence, compensation, and training.

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