Research Scientist Engineer - marine microbial ecology: USA

The School of Oceanography in the College of the Environment has an outstanding opportunity for a Research Scientist Engineer 4.

The School of Oceanography, through the Center for Environmental Genomics (CEG), has developed a novel underway flow cytometer, called SeaFlow, that generates large-scale, high-frequency, multivariate flow cytometry data for individual microbial cells. To map microbial distributions and characteristics, SeaFlow instruments have been deployed on over 60 oceanographic expeditions, collecting data on over 150,000 samples in many parts of the world’s oceans. SeaFlow data has become a critical component of these cruises. The SeaFlow project is a large multi-person effort that requires successful coordination and collaboration with staff, students, and faculty that are located both at the UW and at other universities.

The position

  • reports directly to the principal investigator to analyze both existing data and data being generated while at sea and to help monitor the fleet of instruments during their deployments.
  • general duties of this position are to manage, process, and evaluate SeaFlow data quality, work collaboratively with at- sea operators of the instruments to ensure optimal instrument performance, and implement newly developed software tools for use at sea.
  • requires working knowledge of different software languages such as R or python, experience generating and analyzing flow cytometry data from natural marine samples, working knowledge of size-structured matrix population models, experience in culturing of axenic phytoplankton, and an ability to work collaboratively with software engineers, equipment engineers, marine technicians and scientists from the UW and other universities.
  • requires attention to detail and sea-going experience.

The specific responsibilities fall into the following three general categories.

  • Process and curate data generated by SeaFlow instruments to create different data products that meet sufficient quality standards to be directly input into subsequent analyses pipelines.
  • Requires working knowledge of programming languages, experience working collaboratively with under-development software tools, and sufficient experience with analyzing flow cytometry data to ensure that resulting data products meet expectations.
  • Necessary processing steps include detecting and removing potential artifacts from the raw data files using automated processing combined with visual inspection, ensuring metadata files contain required data sets, processing raw data through data filtration steps to identify particles optimally aligned with laser beam, use and validation of output from population clustering algorithms, and analysis of resulting data products for input into a newly developed size-structured matrix population model used to estimate rates of cell division and net population cell loss in the cyanobacteria Prochlorococcus and Synechococcus population.
  • These processing steps require knowledge of flow cytometric signatures for microbial communities, size-structured matrix population models and the ability to collaborate with software developers, marine technicians, engineers, other researchers that operate SeaFlow at sea, and other researchers that will analyze specific aspects of processed data sets.
  • Monitor SeaFlow instruments remotely during their monthly deployment in Hawaii and on other research cruises. This entails working with the marine technicians or other operators prior to each cruise to ensure that ship-to-shore communication is properly set up and the instrument has been properly calibrated and cleaned.
  • During each cruise, resulting data streams will be monitored to ensure the instrument is properly operated and to inform the science crew about the phytoplankton community structure in real-time.
  • This position will also serve as point of contact as any problems arise during at-sea operation. As needed, travel to / from Hawaii will be required to assist in on-site SeaFlow maintenance.
  • This position will also ensure that the data collected at sea is properly transferred to the SeaFlow data repository at the end of each cruise.
  • Implement and test software tools to provide additional data streams broadcast over the internet in near real-time.
  • Develop and validate size-structured matrix population model to estimate cell division and net population cell loss in the cyanobacteria N2-fixing Crocosphaera. This entails strong experience in culturing of diazotrophic cyanobacteria Crocosphaera and deep knowledge of matrix population models.

The team offers opportunity for gaining new experience and professional growth as the individual develops into the position. As a UW employee, you will enjoy generous benefits and work / life programs. For a complete description of our benefits for this position, please visit our website,


  • PhD in microbiology, biology or related field with at least 4 years of experience in a research setting.
  • Equivalent education / experience will substitute for all minimum qualifications except when there are legal requirements, such as a license / certification / registration.
  • Working knowledge of computer programming languages such as R or Python.
  • Ability to obtain a drivers license.

Equivalent education / experience will substitute for all minimum qualifications except where there are legal requirements such as license / certification / registration.

Desired :

  • Post-PhD research in phytoplankton ecology, biology or related field with at least 4 years research experience in flow cytometry.
  • Working knowledge of size-structured matrix population models.
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