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Dataset Title:  Pterosiphonia bipinnata and Corallina vancouveriensis final experiment shear
and percent remaining at Deadman Bay on San Juan Island, Washington
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_778426)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Subset | Files | Make a graph
 
Variable ?   Optional
Constraint #1 ?
Optional
Constraint #2 ?
   Minimum ?
   or a List of Values ?
   Maximum ?
 
 Treatment (unitless) ?          "High"    "low"
 Shear (Pascals (Pa)) ?          1    20
 PercentRemaining (unitless) ?          0.0    1.0
 Species (unitless) ?          "Corallina"    "Pterosiphonia"
 latitude (degrees_north) ?      
   - +  ?
  < slider >
 longitude (degrees_east) ?      
   - +  ?
  < slider >
 location (unitless) ?      
   - +  ?
 
Server-side Functions ?
 distinct() ?
? ("Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.")

File type: (more info)

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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Treatment {
    String bcodmo_name "treatment";
    String description "High (7.8) or Low (7.3) pH conditions";
    String long_name "Treatment";
    String units "unitless";
  }
  Shear {
    Byte _FillValue 127;
    Byte actual_range 1, 20;
    String bcodmo_name "unknown";
    String description "Shear force applied";
    String long_name "Shear";
    String units "Pascals (Pa)";
  }
  PercentRemaining {
    Float64 _FillValue NaN;
    Float64 actual_range 0.0, 1.0;
    String bcodmo_name "unknown";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "Percentage of spores remaining after assay";
    String long_name "Percent Remaining";
    String units "unitless";
  }
  Species {
    String bcodmo_name "species";
    String description "Latin name of seaweed";
    String long_name "Species";
    String units "unitless";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float64 _FillValue NaN;
    Float64 actual_range 48.51359, 48.51359;
    String axis "Y";
    String bcodmo_name "latitude";
    Float64 colorBarMaximum 90.0;
    Float64 colorBarMinimum -90.0;
    String description "latitude with positive values indicating North";
    String ioos_category "Location";
    String long_name "Latitude";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
    String standard_name "latitude";
    String units "degrees_north";
  }
  longitude {
    String _CoordinateAxisType "Lon";
    Float64 _FillValue NaN;
    Float64 actual_range -123.14893, -123.14893;
    String axis "X";
    String bcodmo_name "longitude";
    Float64 colorBarMaximum 180.0;
    Float64 colorBarMinimum -180.0;
    String description "longitude with negative values indicating West";
    String ioos_category "Location";
    String long_name "Longitude";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
    String standard_name "longitude";
    String units "degrees_east";
  }
  location {
    String bcodmo_name "site";
    String description "name of the location";
    String long_name "Location";
    String units "unitless";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
    String acquisition_description 
"Sporophytic specimens of Pterosiphonia bipinnata and Corallina vancouveriensis
were collected from the mid to low intertidal zone on San Juan Island,
Washington (Deadman Bay: 48 30' 48.93\\\"N, 123 8'56.14\\\"W), immediately
transported to Friday Harbor Laboratories (FHL), and maintained in an outdoor
seawater table for up to one week before testing. Reproductive parent fronds
were held at ambient levels of seawater pH/pCO2 and were only exposed to
experimental conditions while releasing spores. Spore release and settlement
was performed in the Ocean Acidification Environmental Laboratory (OAEL) at
FHL, allowing precise control of pH and temperature in a flow-through system.
Two pH treatments were established by bubbling CO2 (7.75, 7.30 total scale) at
11C and confirmed with carbonate water chemistry analyses. Specifically,
spectrophotometric pH was determined as per SOP6 and total alkalinity was
measured using an open cell titrator as outlined in SOP3b (Dickson et al.
2007). Ambient pH values for the Salish Sea are approximately 7.8, and pH as
low as 7.3 has been documented in nearshore environments in Washington.\\u00a0
 
\\u00a0The spore settlement apparatus consisted of a carriage system that
slowly (1-2.5 cm/hr.) drove reproductive algal thalli across a glass
settlement plate (0.6 x 7.6 x 60 cm), while releasing spores. The working
section (14 x 1.5 cm) was defined at one end of the plate. Spores landing in
the working section had a decreasing gradient of attachment time, determined
by the rate parent thalli were driven across the plate and the time the plate
was allowed to set. Error in attachment time was estimated to be 6-12 minutes
given sinking rates of spores of comparable spore size (50-100 um) and release
height (5-10 cm).
 
The shear flume was designed to release a tall column of water that flushes
quickly across the working section of the spore settlement plate. Water column
height was varied to create a range of shear stresses. \\u00a0Shear stresses
generated by each water column height were calculated according to Schultz et
al. 2000, using the height of the channel (4.3 mm), the pressure gradient
across the working section (measured with a manometer), and the length of the
working section. \\u00a0Most spores were removed in the first 10 seconds of
continuous exposure to shear and longer exposure times result in little
additional detachment, so trials were limited to 15 seconds.\\u00a0
 
Prior to each test, the shear flume was fitted on the settlement plate with
clamps and the released spores were photographed using a microscope
(Steindorff SXC, New York Microscopes) connected to a camera (Nikon Coolpix
S3300), using the lines drawn in the working section for reference. For the
attachment time assay, a low shear stress (1 Pa) was applied and the remaining
spores were photographed and counted.\\u00a0
 
For the attachment strength assay, spores were allowed to set in stationary
water for 35-48 hours in P. bipinnata and for 5-10 hours in C.
vancouveriensis, since maximum attachment of each species was found in these
time frames using the logistic regression analyses of attachment time. For P.
bipinnata, replication was achieved by repeating the experiment in time since
one frond moved across the entire settlement plate in each run. Due to
limitations with C. vancouveriensis spore release, several fronds were used to
provide sufficient spores for this assay. In this case, each frond that
released spores was considered a replicate, and this was repeated across
several days. All spore releases were natural, as attempts to artificially
induce spore release (osmotic, temperature, or light) were unsuccessful.\\u00a0
 
Attached spores were exposed to increasing shear stresses (1, 4, 7, 17 and 20
Pa). Shear stresses in the flume represented boundary layer velocities of 0.2
\\u2013 4 ms-1, similar to intertidal field conditions. At each position and at
each shear stress applied, spores were counted through photo-analysis in
ImageJ (version 1.48; U.S. National Institutes of Health, Bethesda, MD). With
each successive application of shear stress, we expected an increasing
percentage of spores to detach from the settlement plate, up to a maximum
value assuming some spores would be stronger than our assay. The effect of
shear stress on spore detachment in each species was tested using an
exponential rise-to-maximum non-linear regression (SigmaPlot 11.0, R2 = 0.84 -
0.99), which provided estimates of two parameters: the maximum percentage of
spores detached and the initial dependence of detachment on shear stress. The
first derivatives of fitted, non-linear regressions were plotted to estimate
frequency distributions of spore attachment strength.";
    String awards_0_award_nid "55120";
    String awards_0_award_number "OCE-1041213";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1041213";
    String awards_0_funder_name "NSF Division of Ocean Sciences";
    String awards_0_funding_acronym "NSF OCE";
    String awards_0_funding_source_nid "355";
    String awards_0_program_manager "Mary Beth Saffo";
    String awards_0_program_manager_nid "51608";
    String cdm_data_type "Other";
    String comment 
"The effect of pH on the attachment of Corallina vancouveriensis spores final 
  PI: Emily Carrington 
  Version: 2019-10-01";
    String Conventions "COARDS, CF-1.6, ACDD-1.3";
    String creator_email "info@bco-dmo.org";
    String creator_name "BCO-DMO";
    String creator_type "institution";
    String creator_url "https://www.bco-dmo.org/";
    String data_source "extract_data_as_tsv version 2.3  19 Dec 2019";
    String date_created "2019-10-01T19:47:02Z";
    String date_modified "2019-10-29T15:25:03Z";
    String defaultDataQuery "&amp;time&lt;now";
    String doi "10.1575/1912/bco-dmo.778426.1";
    Float64 Easternmost_Easting -123.14893;
    Float64 geospatial_lat_max 48.51359;
    Float64 geospatial_lat_min 48.51359;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -123.14893;
    Float64 geospatial_lon_min -123.14893;
    String geospatial_lon_units "degrees_east";
    String history 
"2020-12-02T12:16:37Z (local files)
2020-12-02T12:16:37Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_778426.html";
    String infoUrl "https://www.bco-dmo.org/dataset/778426";
    String institution "BCO-DMO";
    String instruments_0_acronym "camera";
    String instruments_0_dataset_instrument_description "Prior to each test, the shear flume was fitted on the settlement plate with clamps and the released spores were photographed using a microscope (Steindorff SXC, New York Microscopes) connected to a camera (Nikon Coolpix S3300), using the lines drawn in the working section for reference.";
    String instruments_0_dataset_instrument_nid "778437";
    String instruments_0_description "All types of photographic equipment including stills, video, film and digital systems.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/311/";
    String instruments_0_instrument_name "Camera";
    String instruments_0_instrument_nid "520";
    String instruments_0_supplied_name "camera (Nikon Coolpix S3300)";
    String instruments_1_acronym "Pressure Sensor";
    String instruments_1_dataset_instrument_description "Pressure gradient across the working section (measured with a manometer).";
    String instruments_1_dataset_instrument_nid "778435";
    String instruments_1_description "A pressure sensor is a device used to measure absolute, differential, or gauge pressures.  It is used only when detailed instrument documentation is not available.";
    String instruments_1_instrument_name "Pressure Sensor";
    String instruments_1_instrument_nid "567";
    String instruments_1_supplied_name "manometer";
    String instruments_2_acronym "Water Temp Sensor";
    String instruments_2_dataset_instrument_description "Specifically, spectrophotometric pH was determined as per SOP6 and total alkalinity was measured using an open cell titrator as outlined in SOP3b. As described in Dickson, A.G., Sabine, C.L. and Christian, J.R. (Eds.) 2007. Guide to Best Practices for Ocean CO2 Measurements. PICES Special Publication 3, 191 pp.";
    String instruments_2_dataset_instrument_nid "778451";
    String instruments_2_description "General term for an instrument that measures the temperature of the water with which it is in contact (thermometer).";
    String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/134/";
    String instruments_2_instrument_name "Water Temperature Sensor";
    String instruments_2_instrument_nid "647";
    String instruments_2_supplied_name "Thermometer";
    String instruments_3_acronym "pH Sensor";
    String instruments_3_dataset_instrument_description "Specifically, spectrophotometric pH was determined as per SOP6. As described in Dickson, A.G., Sabine, C.L. and Christian, J.R. (Eds.) 2007. Guide to Best Practices for Ocean CO2 Measurements. PICES Special Publication 3, 191 pp.";
    String instruments_3_dataset_instrument_nid "778434";
    String instruments_3_description "General term for an instrument that measures the pH or how acidic or basic a solution is.";
    String instruments_3_instrument_name "pH Sensor";
    String instruments_3_instrument_nid "674";
    String instruments_3_supplied_name "pH meter";
    String instruments_4_dataset_instrument_description "Prior to each test, the shear flume was fitted on the settlement plate with clamps and the released spores were photographed using a microscope (Steindorff SXC, New York Microscopes) connected to a camera (Nikon Coolpix S3300), using the lines drawn in the working section for reference.";
    String instruments_4_dataset_instrument_nid "778436";
    String instruments_4_description "Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a \"light microscope\".";
    String instruments_4_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB05/";
    String instruments_4_instrument_name "Microscope-Optical";
    String instruments_4_instrument_nid "708";
    String instruments_4_supplied_name "microscope (Steindorff SXC, New York Microscopes)";
    String keywords "bco, bco-dmo, biological, chemical, data, dataset, dmo, erddap, latitude, longitude, management, oceanography, office, percent, PercentRemaining, preliminary, remaining, shear, species, treatment";
    String license "https://www.bco-dmo.org/dataset/778426/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/778426";
    Float64 Northernmost_Northing 48.51359;
    String param_mapping "{'778426': {'lat': 'flag - latitude', 'lon': 'flag - longitude'}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/778426/parameters";
    String people_0_affiliation "University of Washington";
    String people_0_affiliation_acronym "FHL";
    String people_0_person_name "Emily Carrington";
    String people_0_person_nid "51609";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "University of British Columbia";
    String people_1_affiliation_acronym "UBC-Bot";
    String people_1_person_name "Patrick Martone";
    String people_1_person_nid "710046";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "University of British Columbia";
    String people_2_affiliation_acronym "UBC-Bot";
    String people_2_person_name "Rebecca Guenther";
    String people_2_person_nid "710051";
    String people_2_role "Contact";
    String people_2_role_type "related";
    String people_3_affiliation "Woods Hole Oceanographic Institution";
    String people_3_affiliation_acronym "WHOI BCO-DMO";
    String people_3_person_name "Mathew Biddle";
    String people_3_person_nid "708682";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "OA - Ecomaterials Perspective";
    String projects_0_acronym "OA - Ecomaterials Perspective";
    String projects_0_description 
"Effects of Ocean Acidification on Coastal Organisms: An Ecomaterials Perspective
This award will support researchers based at the University of Washington's Friday Harbor Laboratories. The overall focus of the project is to determine how ocean acidification affects the integrity of biomaterials and how these effects in turn alter interactions among members of marine communities. The research plan emphasizes an ecomaterial approach; a team of biomaterials and ecomechanics experts will apply their unique perspective to detail how different combinations of environmental conditions affect the structural integrity and ecological performance of organisms. The study targets a diversity of ecologically important taxa, including bivalves, snails, crustaceans, and seaweeds, thereby providing insight into the range of possible biological responses to future changes in climate conditions. The proposal will enhance our understanding of the ecological consequences of climate change, a significant societal problem.
Each of the study systems has broader impacts in fields beyond ecomechanics. Engineers are particularly interested in biomaterials and in each system there are materials with commercial potential. The project will integrate research and education by supporting doctoral student dissertation research, providing undergraduate research opportunities via three training programs at FHL, and summer internships for talented high school students, recruited from the FHL Science Outreach Program. The participation of underrepresented groups will be broadened by actively recruiting URM and female students. Results will be disseminated in a variety of forums, including peer-reviewed scientific publications, undergraduate and graduate course material, service learning activities in K-8 classrooms, demonstrations at FHL's annual Open House, and columns for a popular science magazine.";
    String projects_0_end_date "2013-08";
    String projects_0_geolocation "Friday Harbor, WA";
    String projects_0_name "Effects of Ocean Acidification on Coastal Organisms: An Ecomaterials Perspective";
    String projects_0_project_nid "2250";
    String projects_0_project_website "http://depts.washington.edu/fhl/oael.html";
    String projects_0_start_date "2010-09";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 48.51359;
    String standard_name_vocabulary "CF Standard Name Table v55";
    String subsetVariables "latitude,longitude,location";
    String summary "Pterosiphonia bipinnata and Corallina vancouveriensis final experiment shear and percent remaining at Deadman Bay on San Juan Island, Washington";
    String title "Pterosiphonia bipinnata and Corallina vancouveriensis final experiment shear and percent remaining at Deadman Bay on San Juan Island, Washington";
    String version "1";
    Float64 Westernmost_Easting -123.14893;
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.

Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names, followed by a collection of constraints (e.g., variable<value), each preceded by '&' (which is interpreted as "AND").

For details, see the tabledap Documentation.


 
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