Category: References
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Updating CalCOFI Hydrographic Database
How to update the CCDB Hydrographic Database in MySQL In addition to ERDDAP, SIO-CalCOFI has a smaller, queryable, online, hydrographic database. This query form includes bottle-related data only and resides at cappuccino.ucsd.edu. These instructions were composed after multiple attempts to update the large mySQL database table with new data. Create a new CCDB data table…
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Nutrient Methods
Nutrient Analysis, Nitrate, Nitrite, Silicate, Phosphate and Ammonium SUMMARY: The phytoplankton macro nutrients nitrate, nitrite, silicate, and phosphate in seawater are analyzed using colorimetric assays. Ammonium concentrations are determined using a fluorometric assay. 1. Principle Nutrient analysis is performed on a QuAAtro continuous segmented flow autoanalyzer (SEAL Analytical). A sample of seawater enters…
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Data Algorithms
CalCOFI hydrographic CTD data, particularly the thermodynamic properties, are computed by Seasoft based on EOS-80. Temperatures, typically from the primary temperature sensor, are merged with bottle sample data into station files which produce the hydrographic database and other data products, Hydrographic Reports, figures, IEHs. CTD sensor salinities, and oxygen values may also replace bottle measurements…
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CTD.csv: Bottle-corrected CTD+Bottle 66-Cols
CTD + Bottle 66-column CSV Column Format (Prelim or Final CTD.csv format – ISUS QC code only) Column Field Description Format 1 Project Cruise; usually CalCOFI Text, variable 2 Study YYMMSS (year month ship) Cruise designation Text, 6 char 3 Ord_Occ Order Occupied Integer 4 Event_Num CTD-at-Depth event number Integer 5 Cast_ID Study+Order Occupied+up or…
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CTD Data Processing Protocol
Please note, the processing methods described use SIO-CalCOFI-developed software (DECODR & BtlVsCTD) to merge and correct Seabird 911+ CTD data with bottle samples. The Seasoft portion of our data processing protocol follow their recommended settings for our 911+ v2 CTD & deck unit. “Sta.csvs” are bottle data collected at each station cast combined with 1m binavg…
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Conductivity to Salinity Algorithms
Bottle Sample Salinity Bottle sample salinities are calculated in both PSal (Portasal Data Acquisition program) and DECODR, software developed by SIO-CalCOFI from Fortran source code by Mantyla & Newton. Visual Basic source code for the calculation of salinity from conductivity : ‘two conductivity values, from two Portasal cell fills; averaging 5 cond readings = 10…
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Suggestions on What to Bring to Sea
Most necessities are provided by the ship but a few amenities can make the cruise more comfortable: Sea sickness medication: If you know you are prone to seasickness, bring any medication you know works for you. Marezine, Meclizine, Bonine, Dramamine or Scopolamine anti-seasick medications are some examples – some work for some people; some have…
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Sta.csv Data Codes
SIO-CalCOFI uses datacodes in the sta.csv bottle data files to define data processing actions & output.
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Fluorometry FAQ
Frequently Asked Questions About Fluorometric Chlorophyll Analysis Q: Why measure chlorophyll? A: All plant life contains the primary photosynthetic pigment chlorophyll a. Microscopic, planktonic plants, or phytoplankton, occupy the lit zone of all water bodies. With over 70% of the surface of the earth covered in water, phytoplankton and photosynthetic bacteria are responsible for almost…
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Net Sample Preservation
After completion of the net tow, concentrate the plankton sample into the cod end by washing down the net with the deck seawater hose (DO NOT use fresh water). Be sure to spray the net from the outside to minimize damage of the delicate plankton in the sample. Once the sample is concentrated into…