Lynker Corporation is expecting the need to hire a Phytoplankton Geneticist and IFCB Engineer to support a contract with NOAA's National Marine Fisheries Service (NMFS) Northwest Fisheries Science Center (NWFSC). This is a full-time position that is anticipated to begin as early as May 1, 2024 and will be based at the NWFSC facility in Seattle, WA with some related field work. Hiring for this position will be contingent on contract award.

The quantity and quality of food for juvenile salmon when they first enter the ocean is important for their growth and survival. This project will develop new indicators of food quality at the base of the marine food web (i.e., phytoplankton) to better parameterize salmon life cycle models, improving estimates of growth, survival, and adult return forecasts. Indicators will be developed using phytoplankton community composition data collected by a robotic microscope (Imaging FlowCytobot [IFCB]) and from environmental DNA (eDNA) sample collections. The IFCB is an automated imaging flow cytometer that generates on the order of 30,000 images of particles (i.e. phytoplankton) per hour in the size range of <10 – 150 µm. Machine learning algorithms are used to automate the taxonomic identification of phytoplankton images obtained by the IFCB. High-throughput sequencing of eDNA samples can be used to determine phytoplankton diversity. A DNA reference database is used to make taxonomic assignments to the sequences and the results are then used to determine differences in phytoplankton diversity in space and time.

The NWFSC requires technical and engineering support services to assist with the collection and processing of IFCB and eDNA samples, develop and manage IFCB and eDNA data pipelines and databases, and assist with IFCB operations and maintenance.

Key tasks of the Phytoplankton Geneticist and IFCB Engineer will include the following:

Task 1 : Collect and analyze eDNA samples.

• Collect and filter water samples - may require participating in fisheries surveys and spending days at sea.
• Extract DNA from archived filters.
• Prepare libraries for DNA sequencing following established protocols involving polymerase chain reaction, agarose gel electrophoresis, magnetic bead cleanup as well as DNA fragment size and quantification analyses.
• Pool libraries for analysis with an Illumina MiSeq benchtop sequencer.
• Prepare and maintain a sample log for eDNA samples.
• Prepare text describing methods and results and prepare summary figures and data tables as requested by the project lead.

Deliverables:

• Sequencing libraries of all eDNA samples prepared for analysis.
• Complete and thorough sample log documenting the eDNA samples collected and processed (e.g. samples filtered, extracted, and prepared for DNA sequencing).
• Draft text, tables, and figures for reports and manuscripts.
• Monthly progress report to include, but not necessarily be limited to, the following: accomplishments, issues encountered, travel (including purpose, significant outcomes, action items), and recommendations, if applicable.

Task 2: Assist with IFCB operations and maintenance.

• Establish secure IFCB communications in the laboratory and field by working cross-functionally with project partners, NWFSC IT specialists, and research vessel technicians.
• Calibrate the IFCB to meet manufacturer's quality assurance and control (QA/QC) specifications.
• Configure IFCB settings (e.g. gain and threshold, binarize threshold, grow settings, background lightness) to optimize sampling of the phytoplankton community of interest as determined by the project lead, and to ensure that they are consistent across instruments and sampling endeavors to maintain data consistency (e.g. account for photomultiplier tube drift and flashlamp aging).
• Configure IFCB's associated hardware infrastructure (e.g. universal power supply, seawater flowthrough) for operations.
• Conduct maintenance and servicing of the IFCB and associated hardware infrastructure, including part replacement and software updates.
• Troubleshoot and repair/correct IFCB failures in a timely fashion to reduce data gaps.

Deliverables:

• Reliable and secure communications infrastructure to support the IFCB user interface and data transfer.
• High-quality IFCB data time series that has minimal data gaps and high consistency between sampling endeavors.
• Monthly progress report to include, but not necessarily be limited to, the following: accomplishments, issues encountered, travel (including purpose, significant outcomes, action items), and recommendations, if applicable.

Task 3: Develop and manage IFCB and eDNA data pipelines and databases.

• In collaboration with NWFSC scientists and project partners, develop and maintain a data pipeline to automate data transfer from the IFCB to local computers, apply machine learning classifiers to process raw data, and display data and data products through the use of existing platforms (such as IFCB dashboard).

• Process MiSeq sequencing results through existing eDNA data pipelines.

• Develop and manage IFCB and eDNA databases that include associated metadata and contextual oceanographic information.

• Backup copies of raw and processed IFCB and eDNA data.

• Archive IFCB and eDNA data in appropriate data repositories.

• Prepare documentation describing IFCB and eDNA data handling procedures.

Deliverables:

• Operational data pipeline within 4 months of the commencement of IFCB operations or within 4 months of the award if IFCB operations are already underway.
• Near real-time visualizations of IFCB data, imagery, and instrument parameters over the web using existing platforms.
• Processed sequencing results.
• IFCB and eDNA databases with associated metadata and contextual oceanographic information that is updated over time as new data are generated, available to the project lead at all times, backed up when edited, and archived in appropriate data repositories.
• Backup copies of IFCB imagery and raw sequencing data on external hard drives or other file management systems determined by the project lead.
• IFCB and eDNA data submitted to appropriate data repositories.
• Documentation describing IFCB and eDNA data handling procedures.
• Monthly progress report to include, but not necessarily be limited to, the following: accomplishments, issues encountered, travel (including purpose, significant outcomes, action items), and recommendations, if applicable.

The Phytoplankton Geneticist and IFCB Engineer selected should meet the following Requirements:

• Bachelor's degree, or higher, from an accredited college or university with a major directly related in a field of study as related to the requirements of specific task order with emphasis in oceanography, marine science, applied ocean sciences/engineering, data science, or similar fields plus two (2) years of experience in related fields or a combination of such totaling six (6) years combined of education and/or experience. A higher level degree (e.g., Master's, PhD) in these fields may be substituted for experience.
• Demonstrated proficiency and experience with programming languages including Linux, Python, R and/or MATLAB.
• Demonstrated proficiency and experience with data management, including database development and management, data entry, and data archiving.
• Demonstrated proficiency in setting up networks.
• Previous experience operating, maintaining, troubleshooting, and servicing advanced scientific instrumentation (or ability to learn).
• Basic laboratory skills including pipetting, sterilization, record keeping, lab safety, and organization.
• Excellent verbal and written communication skills with experience communicating across a range of disciplines.
• Must be able to drive a government vehicle as necessary.

The selected candidates for this position will work up to 40 hours per week. Travel is anticipated for one or two annual research cruises on the west coast, and it may be necessary to travel to Newport, Oregon for project team meetings.

About Lynker

Lynker is a growing, employee owned, small business, specializing in professional, scientific and technical services. Our continually expanding team combines scientific expertise with mature, results-driven processes and tools to achieve technically sound, cost effective solutions in hydrology/water sciences, geospatial analysis, information technology, resource management, conservation, and management and business process improvement.

We focus on putting the right people in the right place to be effective. And having the right people is critical for success. Our streamlined organization enables and empowers our talented professionals to tackle our customers' scientific and technical priorities – creatively and effectively.

Lynker offers a team-oriented work environment, and the opportunity to work in a culture of exceptionally skilled and diverse professionals who embrace sound science and creative solutions. Lynker's benefits include the following:

• Comprehensive healthcare for the employee at no monthly cost
• Healthcare benefit covers medical, prescription drug, dental, and vision
• Personal Time Off (PTO) Policy plus paid holidays
• Highly competitive compensation plan regularly calibrated against industry and location benchmarks
• 401(k) retirement plan with company-matching
• Employee Stock Ownership Plan (ESOP) – we're all company owners!
• Flexible spending accounts
• Employee assistance program (EAP)
• Short- and long-term disability insurance
• Life and accident insurance
• Tuition assistance/Training/Workforce improvement reimbursement per year
• Spot bonuses for exceptional performance
• Annual Employee Recognition Awards with bonuses
• Employee Referral Program
• Free centralized, self-directed Learning Management System to learn at your own pace
• Personalized career growth plans for every employee

Lynker is an E-Verify employer.

Lynker is proud to be an Equal Opportunity Employer and encourages women, minorities, individuals with disabilities and veterans to apply.