clean up

config/_default/hugo.yaml

@@ -4,7 +4,7 @@
 # This file is formatted using YAML syntax - learn more at https://learnxinyminutes.com/docs/yaml/
 
 title: SeaFlow Research Group # Website name
-baseURL: 'https://example.com/' # Website URL
+baseURL: 'https://seaflow.netlify.app/' # Website URL
 
 ############################
 ## LANGUAGE

config/_default/params.yaml

@@ -3,6 +3,9 @@
 # Documentation: https://docs.hugoblox.com/
 # This file is formatted using YAML syntax - learn more at https://learnxinyminutes.com/docs/yaml/
 
+params:
+  ShowDatesOnPosts: true
+
 # Appearance
 
 appearance:
@@ -15,11 +18,11 @@ appearance:
 
 marketing:
   seo:
-    site_type: Organization
-    local_business_type: ''
-    org_name: ''
-    description: 'A highly-customizable Hugo research group theme powered by Wowchemy website builder.'
-    twitter: 'GetResearchDev'
+    site_type: Person
+    local_business_type: 'ProfessionalService'
+    org_name: 'Francois Ribalet'
+    description: 'Francois Ribalet is an oceanographer who develops tools and models to study how microscopic plants in the ocean, phytoplankton, respond to climate change.'
+    twitter: ''
   analytics:
     google_analytics: ''
     baidu_tongji: ''
@@ -72,7 +75,7 @@ features:
   privacy_pack:
     enable: false
   repository:
-    url: 'https://github.com/<username>/<repository>'
+    url: 'https://github.com/seaflow-uw/seaflow-web'
     content_dir: content
     branch: main
   avatar:

content/_index.md

@@ -7,8 +7,8 @@ type: landing
 sections:
   - block: markdown
     content:
-      title: Welcome to the SeaFlow Research Group
-      text: The SeaFlow Research Group is an interdisciplinary team of scientists dedicated to understanding the role of phytoplankton in a changing planet. phytoplankton are the invisible engines of our oceans, driving the biological carbon pump that helps regulate Earth's climate. As our planet faces unprecedented climate change, understanding how these microscopic photosynthetic organisms respond to and influence environmental shifts has become increasingly critical. Our research focuses on developing innovative observational technologies and advanced computational approaches to transform our understanding of how phytoplankton drive and respond to environmental changes. We are committed to open science and reproducible research, and we welcome collaboration with other researchers and organizations.
+      title: The Role of Phytoplankton in a Changing Planet
+      text: The SeaFlow Research Group is an interdisciplinary team of scientists dedicated to understanding the role of phytoplankton in a changing planet. Phytoplankton are the invisible engines of our oceans, driving the biological carbon pump that helps regulate Earth's climate. Our research focuses on developing innovative observational technologies and advanced computational approaches to understand how these microscopic photosynthetic organisms respond to and influence climate change.
 
   - block: slider
     content:
@@ -73,7 +73,7 @@ sections:
     content:
       title: Latest News
       subtitle:
-      text: Transform your phytoplankton research with SeaFlow, our innovative flow cytometer that operates continuously underway. Own a SeaFlow or rent it for your upcoming research expeditions - [contact us](mailto:[email protected]) to discuss your research needs and become a part of the SeaFlow community.
+      text: Transform your phytoplankton research with SeaFlow, our innovative flow cytometer that operates continuously underway. Own a SeaFlow or rent it for your upcoming research expeditions - [contact us](mailto:[email protected]) to discuss your research needs and how to become a part of the SeaFlow community.
         {{% cta cta_link="./instrument/" cta_text="Meet the Instrument →" %}}
 
 

content/authors/admin/_index.md

@@ -60,12 +60,6 @@ social:
   icon_pack: fab
   link: https://github.com/seaflow-uw  
 
-# Link to a PDF of your resume/CV from the About widget.
-# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below.
-# - icon: cv
-#   icon_pack: ai
-#   link: files/cv.pdf
-
 # Enter email to display Gravatar (if Gravatar enabled in Config)
 email: '[email protected]'
 

content/contact/index.md

@@ -7,8 +7,10 @@ type: landing
 sections:
   - block: contact
     content:
-      title: Contact Us
-      text: Dr. François Ribalet <br>
+      title: Join us
+      text: Join our research group as we explore the lives of phytoplankton and their crucial role in the ocean's ecosystem.  We are committed to fostering the next generation of scientists, equipping them with the skills and knowledge to understand how these microscopic organisms are responding to a changing climate.  We welcome talented individuals from all backgrounds, genders, and levels of experience – undergraduates, graduate students, postdoctoral fellows, and visiting scientists.  If you are interested in joining our team, please contact us. <br>
+        <br>
+        Dr. François Ribalet <br>
         School of Oceanography <br>
         University of Washington <br>
         Ocean Science Building <br>

content/instrument/_index.md

@@ -15,6 +15,6 @@ To address the challenges of studying marine phytoplankton in their natural envi
 
 Since 2010, SeaFlow has been deployed on nearly 100 research cruises to collect per cell fluorescence and light scatter data for approximately 800 billion phytoplankton cells less than 5 micron in size. We converted the light scatter data to cell diameter to map out high resolutions distributions of phytoplankton cell size and carbon quotas across 200,000 km of surface ocean and 80 degrees of latitude.  An example dataset from 64 cruise is freely available at [Zenodo](https://doi.org/10.5281/zenodo.2678021.).
 
-**NEW! Own a SeaFlow or rent it for your upcoming research expeditions** - [Contact Us](mailto:[email protected]) to discuss your research needs and become a part of the SeaFlow community.
+**NEW! Own a SeaFlow or rent it for your upcoming research expeditions** - [Contact Us](mailto:[email protected]) to discuss your research needs and how to become a part of the SeaFlow community.
 
 </br>

content/instrument/inventory/index.md

@@ -1,6 +1,8 @@
 ---
 title: Other Information
-lastmod: "2024-01-15"
+date: "2024-01-15"
+show_date: false
+share: false
 ---
 The ship’s real-time feed of position, time, temperature, salinity is broadcast either over the ship’s network and recorded by the SeaFlow computer.
 <!--more--> 

content/instrument/seaflow/_index.md → content/instrument/seaflow/index.md

@@ -1,6 +1,8 @@
 ---
 title: Meet the Instrument
-lastmod: "2024-06-01"
+date: "2024-06-01"
+show_date: false
+share: false
 ---
 
 The SeaFlow instrument is a shipboard underway flow cytometer that provides continuous multi-parameter single particle measurements without the need for clean water. Detailed information can be found in [Swalwell et al. (2011)](https://doi.org/10.4319/lom.2011.9.466).

content/publication/beckett-2024/index.md

@@ -10,4 +10,5 @@ projects : []
 tags : []
 doi : "10.1038/s41467-024-46165-3"
 math : false
+share : false
 ---

content/publication/boysen-2021/index.md

@@ -10,4 +10,5 @@ projects : []
 tags : []
 doi : "10/grzmhn"
 math : false
+share : false
 ---

content/publication/carlson-2022/index.md

@@ -11,5 +11,6 @@ projects : []
 tags : []
 doi : "10.1038/s41564-022-01088-x"
 math : false
+share : false
 ---
 

content/publication/coesel-2021/index.md

@@ -9,5 +9,7 @@ featured: false
 publication: "*Proceedings of the National Academy of Sciences*"
 url_pdf: "http://www.pnas.org/lookup/doi/10.1073/pnas.2011038118"
 doi: "10.1073/pnas.2011038118"
+share : false
+
 ---
 

content/publication/connell-2020/index.md

@@ -9,5 +9,7 @@ featured: false
 publication: "*Aquatic Microbial Ecology*"
 url_pdf: "https://www.int-res.com/abstracts/ame/v85/p167-181/"
 doi: "10.3354/ame01950"
+share : false
+
 ---
 

content/publication/dugenne-2023/index.md

@@ -10,4 +10,6 @@ projects : []
 tags : []
 doi : "10.1029/2022GB007386"
 math : false
+share : false
+
 ---

content/publication/dutkiewicz-2024/index.md

@@ -10,4 +10,6 @@ projects : []
 tags : []
 doi : "10.1002/lno.12555"
 math : false
+share : false
+
 ---

content/publication/follett-2022/index.md

@@ -9,5 +9,7 @@ featured: false
 publication: "*Proceedings of the National Academy of Sciences*"
 url_pdf: "https://www.pnas.org/content/119/2/e2110993118"
 doi: "10.1073/PNAS.2110993118"
+share : false
+
 ---
 

content/publication/gradoville-2020/index.md

@@ -9,5 +9,7 @@ featured: false
 publication: "*Limnology and Oceanography*"
 url_pdf: "https://aslopubs.onlinelibrary.wiley.com/doi/full/10.1002/lno.11423"
 doi: "10.1002/lno.11423"
+share : false
+
 ---
 

content/publication/halperin-2013/index.md

@@ -9,5 +9,6 @@ featured: false
 publication: "*ACM International Conference Proceeding Series*"
 tags: ["Design", "Experimentation", "Human factors", "Management"]
 doi: "10.1145/2484838.2484880"
+share : false
 ---
 

content/publication/hamilton-2017/index.md

@@ -1,5 +1,5 @@
 ---
-title: "Dynamics of Teleaulax -like cryptophytes during the decline of a red water bloom in the Columbia River Estuary"
+title: "Dynamics of Teleaulax-like cryptophytes during the decline of a red water bloom in the Columbia River Estuary"
 date: 2017-01-01
 publishDate: 2020-03-09T17:46:51.929393Z
 authors: ["M. Hamilton", "G.M.M. Hennon", "R. Morales", "J. Needoba", "T.D. Peterson", "M. Schatz", "J. Swalwell", "E.V. Armbrust", "F. Ribalet"]
@@ -9,5 +9,6 @@ featured: false
 publication: "*Journal of Plankton Research*"
 tags: ["Mesodinium rubrum", "SeaFlow", "Teleaulax", "cryptophytes", "division rates"]
 doi: "10.1093/plankt/fbx029"
+share : false
 ---
 

content/publication/heal-2017/index.md

@@ -9,5 +9,6 @@ featured: false
 publication: "*Proceedings of the National Academy of Sciences of the United States of America*"
 tags: ["B 12", "Cobalamin", "Cyanobacteria", "Pseudocobalamin", "Thaumarchaeota"]
 doi: "10.1073/pnas.1608462114"
+share : false
 ---
 

content/publication/heal-2021/index.md

@@ -1,5 +1,5 @@
 ---
-title : "Marine Community Metabolomes Carry Fingerprints of Phytoplankton Community Composition"
+title : "Marine community metabolomes carry fingerprints of phytoplankton community composition"
 date : 2021-04-06
 publishDate: 2021-06-01T17:46:51.934135Z
 authors : ["Katherine R. Heal", "Bryndan P. Durham", "Angela K. Boysen", "Laura T. Carlson", "Wei Qin", "Francois Ribalet", "Angelicque E. White", "Randelle Bundy", "E. Virginia Armbrust", "Anitra E. Ingalls"]

content/publication/henderikx-2020/index.md

@@ -9,5 +9,6 @@ featured: false
 publication: "*Applied Optics*"
 url_pdf: "https://doi.org/10.1364/AO.394123"
 doi: "10.1364/AO.394123"
+share : false
 ---
 

content/publication/howard-2017/index.md

@@ -9,5 +9,6 @@ featured: false
 publication: "*Global Biogeochemical Cycles*"
 tags: ["argon", "carbon flux", "gross primary production", "net community production", "oxygen", "triple oxygen isotopes"]
 doi: "10.1002/2016GB005488"
+share : false
 ---
 

content/publication/howe-2013/index.md

@@ -9,5 +9,6 @@ featured: false
 publication: "*Computing in Science and Engineering*"
 tags: ["database applications", "scientific computing", "scientific databases", "workflow management"]
 doi: "10.1109/MCSE.2013.42"
+share : false
 ---
 

content/publication/hynes_2024/index.md

@@ -6,8 +6,7 @@ publication_types : ["2"]
 publication : "in *Limnology and Oceanography*"
 abstract : "The Hawaii Ocean Time-series (HOT) at Station ALOHA (22.75°N, 158°W) in the North Pacific Subtropical Gyre (NPSG) serves as a critical vantage point for observing plankton biomass production and its ecological implications. However, the HOT program's near-monthly sampling frequency does not capture shorter time scale variability in phytoplankton populations. To address this gap, we deployed the SeaFlow flow cytometer for continuous monitoring during HOT cruises from 2014 to 2021. This approach allowed us to examine variations in the surface abundance and cell carbon content of specific phytoplankton groups: the cyanobacteria Prochlorococcus, Synechococcus, and Crocosphaera as well as a range of small eukaryotic phytoplankton (≤ 5 μm). Our data showed that daily to monthly variability in Prochlorococcus and Synechococcus abundance matches seasonal and interannual variability, while small eukaryotic phytoplankton and Crocosphaera showed the highest seasonal and interannual fluctuations. The study also found that eukaryotic phytoplankton and Crocosphaera had higher median cellular growth rates (0.076 and 0.090h−1, respectively) compared to Prochlorococcus and Synechococcus (0.037 and 0.045h−1, respectively). These variances in abundance and growth rates indicate that shifts in the community structure significantly impact primary productivity in the NPSG. Our results underscore the importance of daily to monthly phytoplankton dynamics in ecosystem function and carbon cycling."
 featured : false
-projects : []
-tags : []
+share : false
 doi : "10.1002/lno.12683"
 math : false
 ---

content/publication/hyrkas-2016/index.md

@@ -7,7 +7,7 @@ publication_types: ["2"]
 abstract: "Motivation: Recent technological innovations in flow cytometry now allow oceanographers to collect high-frequency flow cytometry data from particles in aquatic environments on a scale far surpassing conventional flow cytometers. The SeaFlow cytometer continuously profiles microbial phytoplankton populations across thousands of kilometers of the surface ocean. The data streams produced by instruments such as SeaFlow challenge the traditional sample-by-sample approach in cytometric analysis and highlight the need for scalable clustering algorithms to extract population information from these large-scale, high-frequency flow cytometers.Results: We explore how available algorithms commonly used for medical applications perform at classification of such a large-scale, environmental flow cytometry data. We apply large-scale Gaussian mixture models to massive datasets using Hadoop. This approach outperforms current state-of-the-art cytometry classification algorithms in accuracy and can be coupled with manual or automatic partitioning of data into homogeneous sections for further classification gains. We propose the Gaussian mixture model with partitioning approach for classification of large-scale, high-frequency flow cytometry data."
 featured: false
 publication: "*Bioinformatics*"
-tags: ["r28958"]
+share : false
 url_pdf: "http://bioinformatics.oxfordjournals.org/content/32/3/417.abstract"
 doi: "10.1093/bioinformatics/btv594"
 ---

content/publication/hyun-2023/index.md

@@ -6,8 +6,7 @@ publication_types : ["2"]
 publication : "in *Annals of Applied Statistics*"
 abstract : "The ocean is filled with microscopic microalgae, called phytoplankton, which together are responsible for as much photosynthesis as all plants on land combined. Our ability to predict their response to the warming ocean relies on understanding how the dynamics of phytoplankton populations is influenced by changes in environmental conditions. One powerful technique to study the dynamics of phytoplankton is flow cytometry which measures the optical properties of thousands of individual cells per second. Today, oceanographers are able to collect flow cytometry data in real time onboard a moving ship, providing them with fine-scale resolution of the distribution of phytoplankton across thousands of kilometers. One of the current challenges is to understand how these small- and large-scale variations relate to environmental conditions, such as nutrient availability, temperature, light and ocean currents. In this paper we propose a novel sparse mixture of multivariate regressions model to estimate the time-varying phytoplankton subpopulations while simultaneously identifying the specific environmental covariates that are predictive of the observed changes to these subpopulations. We demonstrate the usefulness and interpretability of the approach using both synthetic data and real observations collected on an oceanographic cruise conducted in the northeast Pacific in the spring of 2017."
 featured : true
-projects : []
-tags : []
+share : false
 doi : "10.1214/22-AOAS1631"
 math : false
 ---

content/publication/jones-2021/index.md

@@ -9,5 +9,6 @@ featured: false
 publication: "*Methods in Ecology and Evolution*"
 url_pdf: " https://doi.org/10.1111/2041-210X.13647"
 doi: "10.1111/2041-210X.13647"
+share : false
 ---
 

content/publication/joneskellett-2024/index.md

@@ -6,8 +6,7 @@ publication_types : ["2"]
 publication : "in *ISME Communications*"
 abstract : "Marine microbial ecologists seek measurements of organismal abundance and diversity at high taxonomic resolution to understand ecosystem state and function. Conventional flow cytometry accurately estimates microbial cell abundance but only discerns broad groups with distinct optical properties. While amplicon sequencing resolves more comprehensive diversity within microbiomes, it typically only provides relative organismal abundances within samples, not absolute abundance changes. Internal genomic standards offer a solution for absolute amplicon-based measures. Here, we spiked genomic standards into plankton samples from surface seawater, gathered at 46-kilometer intervals along a cruise transect spanning the southern California Current System and the oligotrophic North Pacific Subtropical Gyre. This enabled evaluation of the absolute volumetric gene copy abundances of 16S rRNA Amplicon Sequence Variants (amplified with 515Y-926R universal primers, quantitatively validated with mock communities) and cell abundances of picocyanobacteria with known genomic 16S copy numbers. Comparison of amplicon-derived cell abundances of Prochlorococcus and Synechococcus with flow cytometry data from nearby locations yielded nearly identical results (slope = 1.01; Pearson’s r = 0.9942). Our findings show that this amplicon sequencing protocol combined with genomic internal standards accurately measures absolute cell counts of marine picocyanobacteria in complex field samples. By extension, we expect this approach reasonably estimates volumetric gene copies for other amplified taxa in these samples."
 featured : false
-projects : []
-tags : []
+share : false
 doi : "10.1093/ismeco/ycae115"
 math : false
 ---

content/publication/juranek-2020/index.md

@@ -1,5 +1,5 @@
 ---
-title: "The Importance of the Phytoplankton “Middle Class” to Ocean Net Community Production"
+title: "The importance of the phytoplankton “middle class” to ocean net community production"
 date: 2020-11-25
 publishDate: 2020-11-25T17:46:51.934135Z
 authors: ["L. Juranek", "A. White", "M. Dugenne", "F. Henderikx Freitas", "S. Dutkiewicz", "F. Ribalet", "S. Ferron", "E.V. Armbrust", "D.M. Karl"]
@@ -9,5 +9,6 @@ featured: false
 publication: "*Global Biogeochemical Cycles*"
 url_pdf: "https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020GB006702"
 doi: "10.1029/2020GB006702"
+share : false
 ---
 

content/publication/liefer-2024/index.md

@@ -6,8 +6,7 @@ publication_types : ["2"]
 publication : "in *Proceedings of the National Academy of Sciences*"
 abstract : "The proportions of carbon (C), nitrogen (N), and phosphorus (P) in surface ocean particulate matter deviate greatly from the canonical Redfield Ratio (C:N:P = 106:16:1) in space and time with significant implications for global carbon storage as this matter reaches the deep ocean. Recent work has revealed clear latitudinal patterns in C:N:P, yet the relative importance of ecological, physiological, or biochemical processes in creating these patterns is unclear. We present high-resolution, concurrent measurements of particulate C:N:P, macromolecular composition, environmental conditions, and plankton community composition from a transect spanning a subtropical-subpolar boundary, the North Pacific Transition Zone. We find that the summed contribution of macromolecules to particulate C, N, and P is consistent with, and provides interpretation for, particulate C:N:P patterns. A decline in particulate C:N from the subtropical to subpolar North Pacific largely reflects an increase in the relative contribution of protein compared to carbohydrate and lipid, whereas variation in C:P and N:P correspond to shifts in protein relative to polyphosphate, DNA, and RNA. Possible causes for the corresponding trends in C:N and macromolecular composition include physiological responses and changes in community structure of phytoplankton, which represented approximately 1/3rd of particulate C across the transect. Comparison with culture experiments and an allocation-based model of phytoplankton macromolecular composition suggest that physiological acclimation to changing nutrient supply is the most likely explanation for the latitudinal trend in C:N, offering both a mechanistic interpretation and biochemical basis for large-scale patterns in C:N:P."
 featured : false
-projects : []
-tags : []
+share : false
 doi : "10.1073/pnas.2404460121"
 math : false
 ---

content/publication/marchetti-2009/index.md

@@ -8,5 +8,6 @@ abstract: "Primary productivity in 30-40% of the world's oceans is limited by av
 featured: false
 publication: "*Nature*"
 doi: "10.1038/nature07539"
+share : false
 ---