{"id":341,"date":"2011-01-01T00:00:01","date_gmt":"2011-01-01T00:00:01","guid":{"rendered":"https:\/\/info.calcofi.com\/2011\/01\/01\/methods-timeline\/"},"modified":"2011-01-01T00:00:01","modified_gmt":"2011-01-01T00:00:01","slug":"methods-timeline","status":"publish","type":"post","link":"https:\/\/mindwander.com\/index.php\/2011\/01\/01\/methods-timeline\/","title":{"rendered":"Methods Timeline"},"content":{"rendered":"

CalCOFI Time Series data are over 67 years old. New adopted practices, methods, software and hardware are thoroughly tested to maintain dataset continuity as the program & science evolves. Core measurements are maintained and many new measurements added. CTD temperature sensors, for example, provide data at a much higher resolution than a 20 bottle hydrocast equipped with reversing thermometers pre-9308 (Aug 1993).<\/p>\n

Although the CTDs casts on CalCOFI started in 1990, CTD-rosette casts did not replace bottles-on-wire hydro casts completely until Aug 1993 (9308). In 2004, LTER joined the CalCOFI cruises, expanding the seawater analyses, adding new measurements.<\/p>\n

Changes of standard practices, methods, software, & equipment will be tabulated here, particularly those affecting the hydrographic data or other data products.<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
 Cruise\/Date<\/span><\/span><\/th>\n\n

 Measurement, 
\n\t\t\t Equipment,  Method<\/span><\/span><\/p>\n<\/th>\n

 Changes    <\/span><\/span><\/th>\n\n

Comments<\/span><\/span><\/p>\n<\/th>\n<\/tr>\n<\/thead>\n

CalCOFI Methods Timeline<\/caption>\n
 \"\"<\/span><\/td>\nMethods Timeline Started<\/td>\n <\/td>\n\n

This page is ‘dynamic’ so new items will be added whenever new methods, measurements, equipment are implemented. Older changes will be added as time-permits and they are remembered.<\/span><\/p>\n<\/td>\n<\/tr>\n

1708SR<\/td>\nCCE-LTER ISUS upgraded to fw v3<\/td>\nISUS upgraded to firmware v3<\/td>\nSeabird acquired Satlantic and took several month to get ISUS service online. Once done, they upgraded the CCE-LTER MBARI-ISUS v2 to firmware v3. Allows easy in-house or at-sea calibration.<\/td>\n<\/tr>\n
1708SR<\/td>\nOxygen Stable Isotope<\/td>\nSeawater samples collected for OSI<\/td>\n5ml of seawater collected from two depths (10m & 50m) on 18 stations<\/td>\n<\/tr>\n
1701RL
\n\t\t\t1704SH<\/td>\n		LARS rosette<\/td>\n24-btl LARS rosette used<\/td>\nEven though RV Reuben Lasker & FSV Bell M Shimada do not have a LARS CTD deployment system, the height clearance allows the use of the LARS rosette. SIO-CalCOFI will use this rosette as primary unless the height clearance becomes a problem, such as on RV Ocean Starr.<\/td>\n<\/tr>\n
1611SR<\/td>\nFirst RV Sally Ride<\/td>\nSIO RV Sally Ride used for CalCOFI<\/td>\nRV Sally Ride used for the first time to do CalCOFI station work; acoustics operational but not calibrated<\/td>\n<\/tr>\n
1611SR<\/td>\nRINKO III Optode<\/td>\nRINKO III Oxygen sensor deployed<\/td>\nOptode used on non-basin stations deeper than 500m, where altimeter was not needed<\/td>\n<\/tr>\n
1611SR<\/td>\nSeawater samples<\/td>\nDomoic Acid & Th-234<\/td>\nCollected ancillary seawater & deploy insitu pumping system<\/td>\n<\/tr>\n
pre-1611SR<\/td>\nISUS (Frank’s) Repaired<\/td>\nPeter Frank’s ISUS repaired & upgraded to firmware v3<\/td>\nISUS was not working so it was sent to Satlantic who repaired it and upgraded the firmware to v3<\/td>\n<\/tr>\n
1609SR<\/td>\nNew research vessel<\/td>\nSIO RV Sally Ride test for CalCOFI<\/td>\nShakedown cruise for RV Sally Ride to do CalCOFI – new LARS, epoxy-coated rosette deployed<\/td>\n<\/tr>\n
1609SR<\/td>\nLARS epoxy-coated rosette<\/td>\nFirst use of new 24-bottle rosette<\/td>\n24-btl white epoxy coated aluminum rosette deployed with stainless steel LARS support<\/td>\n<\/tr>\n
1607OS<\/td>\nSeawater Samples<\/td>\nDomoic Acid samples collected<\/td>\nAncillary seawater sample collection<\/td>\n<\/tr>\n
1604SH<\/td>\nNutrient Analysis<\/td>\nNew (returning) in-house nutrient chemist<\/td>\nNutrients run by SIO-CalCOFI analyst DGS<\/span><\/td>\n<\/tr>\n
1507OC<\/span><\/span><\/td>\nUnderway Measurements<\/td>\nRV Oceanus MET system logs data into individual data files; combined data are unavailable unless merged manually<\/span><\/td>\nUnlike other UNOLS vessels, particularly SIO RV New Horizon, the underway TSG & meterological data are logged at 1Hz into individual files. A combinded data file will have to be generated post-cruise by merging individual sensor data files using the common UTC timestamp. Software pending…<\/span><\/td>\n<\/tr>\n
1504NH<\/span><\/td>\nUnderway Measurements<\/td>\nPCO2<\/sub> and pH measurements added to CCE-LTER suite<\/td>\n\n

 <\/p>\n<\/td>\n<\/tr>\n

1504NH<\/span><\/td>\nNutrient Analysis<\/td>\nStandard matrix; sample vials<\/td>\n\n

Standards now prepared in low nutrient seawater (collected from the end of lines 93.3 or 90.0 and processed with UV light, filtration and aged before use).  New 30 mL polypropylene tubes in use.<\/span><\/p>\n<\/td>\n<\/tr>\n

06 Aug 2014<\/span><\/td>\ncalcofi.com<\/td>\ncalcofi.com 2014 online<\/td>\n\n

Developmental site web.calcofi.com replaces Joomla 1.5 calcofi.com; Joomla 3+ fully implemented. calcofi.com old site moved to old.calcofi.com<\/span><\/p>\n<\/td>\n<\/tr>\n

1402SH<\/span><\/td>\nNutrient Analysis<\/td>\nNew in-house Nutrient Technician<\/td>\n\n

Nutrients run by SIO-CalCOFI analyst LJE.<\/span><\/p>\n<\/td>\n<\/tr>\n

1402SH<\/span><\/td>\nNCOG DNA\/RNA<\/td>\nNCOG sample collection started<\/td>\nNCOG DNA\/RNA samples collected at ~4 depths (10m, chl max, 170m, 515m)<\/td>\n<\/tr>\n
1311NH<\/span><\/td>\nDIC measurments<\/td>\nSampling expands<\/td>\n\n

Dissovled inorganic carbon samples are now drawn at more locations along the cruise track with 14 profile and 8 additional surface water stations per cruise.<\/span><\/p>\n<\/td>\n<\/tr>\n

1211NH<\/td>\nRinko Oxygen Optode<\/td>\nRINKO III Optode deployed<\/td>\nRINKO III Oxygen Optode sensor replaced 2nd SBE43 oxygen sensors on stations where the altimeter was not needed – non-basin stations deeper that 500m.<\/td>\n<\/tr>\n
01Mar2013<\/span><\/td>\nweb.calcofi.com website update<\/td>\nUpgrading calcofi.com to latest Joomla<\/td>\n\n

web.calcofi.com started to migrate calcofi.com 1.5 to 3.0; to improve responsiveness with new dynamic templates – desktop, tablet, and smartphone auto-formatting. Security improvements, auto-updating, jQuery & other new features of version 3.+<\/span><\/p>\n<\/td>\n<\/tr>\n

1207OS<\/span><\/td>\nNutrient Analysis<\/td>\nNew in-house Nutrient Technician<\/td>\n\n

Nutrients run by former ODF chemist, now a SIO-CalCOFI analyst MTM.<\/span><\/p>\n<\/td>\n<\/tr>\n

01May2012<\/span><\/td>\ndev.calcofi.com blog started<\/td>\nSIO-CalCOFI Technical Group developmental blog started.<\/td>\n\n

For metadata: documenting changes in software, data-processing methods, formats, products, & practices.<\/span><\/p>\n<\/td>\n<\/tr>\n

1203SH<\/span><\/td>\nNutrient Analysis<\/td>\nInstrument and analyst change, new Seal QuAAtro Analyzer purchased.<\/td>\n\n

Transitioned to in-house nutrient analysis on new Seal QuAAtro Nutrient Analyzer, nutrients run by SIO-CalCOFI analyst DNF.  Replacing sample analysis by ODF chemist on an AA3 analyzer.<\/span><\/p>\n

Standards now prepared in artificial seawater.<\/span><\/p>\n

NO3 data calculated using regression coefficients from ISUS voltage vs NO3 for 1202NH & 1203SH look nearly identical.<\/span><\/p>\n<\/td>\n<\/tr>\n

1203SH<\/span><\/td>\natsea.calcofi.com blog online<\/td>\nSetup to keep notes during quarterly cruises, particularly those related to data, equipment, & generally noteworthy.<\/td>\n\n

Connected-linked to CalCOFI’s Twitter feed<\/span><\/p>\n<\/td>\n<\/tr>\n

1202NH<\/span><\/td>\nNutrient Analysis<\/td>\n Last cruise where nutrients were run by ODF chemist on an AA3 analyzer.<\/td>\n\n

 <\/p>\n<\/td>\n<\/tr>\n

1202NH+<\/td>\nData Processing<\/td>\nIEH retired as primary data processing file format. Sta.csvs and casts.csv adopted.<\/td>\nAfter parallel-processing (IEH & csv file format) 1104, 1108, 1110 cruise data. Sta.csvs & casts.csv data processing is being used to process, merge, quality-control, publish all hydrographic data. IEH-format is a data product along with the hydrographic database.<\/td>\n<\/tr>\n
1108<\/span><\/td>\nAll measurements & data products<\/td>\nHydrographic data are processed using both old & new methods and compared.<\/td>\n\n

The cruise is once again processed twice, in parallel, using the IEH old-school method and the new csv-format method. GTool development & refinement continues as sta.csvs & casts.csv formats are improved. Final data products are compared for agreement. This is the first cruise to generate data products using new csv-database data processing methods not based on IEHs.<\/span><\/p>\n<\/td>\n<\/tr>\n

1104<\/span><\/td>\nGTool Matlab program developed<\/td>\nSIO-CalCOFI Technical Team implement a new graphical matlab tool to point-check CalCOFI hydrographic data<\/td>\n\n

MGS, in cooperation with the CCTG, develops GTool to replace Andyplots, our legacy method to visually inspect all bottle data on one figure. CTD continuous data are plotted with bottle parameters to cross-check and eliminate fliers.<\/span><\/p>\n<\/td>\n<\/tr>\n

1104<\/span><\/td>\nAll measurements; data products<\/td>\nHydrographic data are processed using both old & new methods and compared.<\/td>\n\n

The cruise is processed twice, in parallel, using the IEH old-school method and the new csv-format method. GTool, a matlab plotting & data-quality control program script, is developed to ingest CTD & sta.csvs to graphically assess CTD & bottle data-quality. Final data products are compared for agreement. This should be the last cruise processed using 00\/20\/22 & IEHs.<\/span><\/p>\n<\/td>\n<\/tr>\n

1101<\/td>\nReported standard level O2<\/td>\nCTD primary or secondary oxygen sensor bottle–corrected measurements are reported instead of interpolated standard level (ISL) oxygen values <\/span><\/span><\/td>\nPretains to final, standard-level bottle data reported in all data products – with the reliability of the SBE 43 oxygen sensors and consistently high data quality when calibrated bi-yearly (twice\/year) and bottle-corrected. Bottle-corrected CTD primary or secondary oxygen values (whichever sensor is performing better that cast) are reported instead of interpolated (calculated) standard level bottle oxygen values.<\/span><\/td>\n<\/tr>\n
1101<\/span><\/td>\n Data storage format, ieh phase out begins; all measurements affected<\/td>\nSta.csv & casts.csv implementation begins, replacing 00\/20\/22 & IEH data process methodology. IEH-method is used as CSV-method is developed.<\/td>\n\n

Bottle data & CTD data processing up til now have been relatively separate although data-quality cross-check are common. Other than CTD temperatures, all hydrographic data reported in IEHs or hydrographic database are bottle sample measurements. In 2011, our new data processing strategy merges the bottle & CTD starting at seawater sample collection. CESL generates individual sta.csvs combining CTD & bottle data immediately after seawater sample collection. Casts.csv is also generated and contains station specific information, replacing the Station Cast Description & Weather files (stacst & weather).<\/span><\/p>\n<\/td>\n<\/tr>\n

1101<\/span><\/td>\n DECODR<\/td>\nDECODR migration to the new sta.csv and casts.csv data-processing scheme in full development<\/td>\n\n

DECODR (Data Entry & Compile Oceanographic Data Reports) program modules are adapted to process either old or new hydrographic data formats. Sta.csvs & casts.csv adaptations are implemented and different data products are generated directly or by generating an IEH first then data products.<\/span><\/p>\n<\/td>\n<\/tr>\n

0901<\/span><\/td>\n DIC measurements resume<\/td>\nDIC (dissolve inorganic carbon) sampling resume after a hiatus.<\/td>\n\n

DIC, aka Keeling, samples were commonly taken on two CalCOFI stations but the new sampling scheme covers several additional stations and depths.<\/span><\/p>\n<\/td>\n<\/tr>\n

2008<\/span><\/td>\n Nutrient Analysis<\/td>\nBegan ammonium analysis<\/td>\n\n

Nutrient analysis expanded to include ammonium.<\/span><\/p>\n<\/td>\n<\/tr>\n

0701<\/span><\/td>\n Salinity measurement<\/td>\nSalReCap – Salinity Record & Capture program introduced, replacing the PSal (DOS shell executable).<\/td>\n\n

SalReCap, Windows program developed by SIO-CalCOFI, replaces ODF-developed PSal, a DOS executable. Immediate comparisons to CTD salinities during analysis becomes available.<\/span><\/p>\n<\/td>\n<\/tr>\n

Apr-05<\/span><\/td>\n Primary Productivity<\/td>\nNew specific activity procedure<\/td>\nThe procedure for calculating cruise 14C specific activity for the productivity assay was changed to reflect daily 14C additions averaged over the course of a cruise.  The six dark bottles have one milliliter removed, added to ethanolamine spiked scintillation cocktail for counting.  Previously specific activity was calculated for a batch of stock and used for the entire cruise.  The new method served to check pipeting, inoculation amounts and any changes in volatile 14C stocks.<\/td>\n<\/tr>\n
0411<\/span><\/td>\n Ancillary measurements such as HPLC, DOM, Size fractionations, Epifluorescence<\/td>\nLTER affiliation on CalCOFI cruises begins<\/td>\n\n

CCE-LTER (California Current Ecosystem Long Term Ecological Research Site) is established and LTER participation on all CalCOFIs begins. A large suite of additional measurements, particularly seawater samples from the rosette, and PRPOOS vertical plankton tow are added to CalCOFI hydrography.<\/span><\/p>\n<\/td>\n<\/tr>\n

0310<\/span><\/td>\n Oxygen measurement<\/td>\nAutotitrator replaces manual modified Winkler titrations<\/td>\n\n

After substantial assay-comparative testing, an ODF-developed oxygen auto-titrator is used to titrate discrete, rosette-bottle, seawater oxygen samples at-sea. New oxygen data format & data processing module is introduced in DECODR.<\/span><\/p>\n<\/td>\n<\/tr>\n

0204<\/span><\/td>\n CalCOFI Data Report<\/td>\nLast bound hardcopy of the bi-annual CalCOFI Hydrographic Data Report is published, CC Reference 03-01 31 July 2003<\/td>\n\n

CalCOFI Hydrographic Data Reports will continue being published electronically as pdfs for global distribution. Bound hardcopies, sent my mail, to different libraries & institutions will stop.<\/span><\/p>\n<\/td>\n<\/tr>\n

0104<\/span><\/td>\n Chlorophyll measurement<\/td>\nFLog, chlorophyll data logging fluorometer program introduced<\/td>\n\n

Prior to FLog, our 24+hr acetone cold-extracted chlorophyll samples were manually logged by hand to a sample form then key-entered into CODES. FLog records fluorometer values automatically in a data-processing friendly format so no transcription is required.<\/span><\/p>\n<\/td>\n<\/tr>\n

Jun 2001<\/td>\nSeasave for Windows<\/td>\nSeabird releases Windows versions<\/td>\nSeasoft\/Seasave & SBE Data Processing software for Windows 98\/NT  released by Seabird<\/td>\n<\/tr>\n
2000<\/span><\/td>\n CTD Fluorometer<\/td>\nSeapoint Fluorometer<\/td>\n\n

Seapoint Chlorophyll Fluorometer in use.<\/span><\/p>\n<\/td>\n<\/tr>\n

9807 (Jul 1998)<\/td>\nCTD Seasave<\/td>\nCon file readable by Seasave v5<\/td>\ncon files prior to 9807 will not open it Windows SBE Data Processing software v5 or v7<\/td>\n<\/tr>\n
9308<\/span><\/td>\n Temperature measurement<\/td>\n4sec ave (prior to bottle closure) CTD temperatures replace reversing thermometer measurements<\/td>\n\n

CTD temperatures are the only measurement entering the hydrographic timeseries (until 2011 when CTD standard level temperature, salinity, & oxygen replace interpolated values).<\/span><\/p>\n<\/td>\n<\/tr>\n

9308<\/span><\/td>\n Seabird CTD-Rosette w\/ 24-10L Niskin-type PVC Bottles<\/td>\nReplace 20 bottle hydro cast & 6 bottle prodo cast<\/td>\n\n

10L Niskin-like bottle constructed by Research support have plastic-coated springs, nylon lanyards, Viton or nitrile o-rings. No metal, rubber, or latex come incontact with seawater samples. Bottles are disassembeld &  ‘productivity-cleaned’ between cruises.<\/span><\/p>\n<\/td>\n<\/tr>\n

1993<\/span><\/td>\n CTD Fluorometer<\/td>\nSeaTech Fluorometer<\/td>\n\n

1993-2000<\/span><\/p>\n<\/td>\n<\/tr>\n

1973<\/span><\/td>\n Chlorophyll measurement<\/td>\nBegan<\/td>\n\n

Discrete chlorophyll analysis was added to the hydrographic dataset.<\/span><\/p>\n<\/td>\n<\/tr>\n

1961<\/span><\/td>\n Nutrient Analysis<\/td>\nExpands beyond phosphate<\/td>\n\n

Nutrient analysis expanded to include silicate, nitrate and nitrite.<\/span><\/p>\n<\/td>\n<\/tr>\n

 <\/td>\n <\/td>\n <\/td>\n\n

 <\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n","protected":false},"excerpt":{"rendered":"

CalCOFI Time Series data are over 67 years old. New adopted practices, methods, software and hardware are thoroughly tested to maintain dataset continuity as the program & science evolves. Core measurements are maintained and many new measurements added. CTD temperature sensors, for example, provide data at a much higher resolution than a 20 bottle hydrocast […]<\/p>\n","protected":false},"author":1,"featured_media":303,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[19],"tags":[],"class_list":["post-341","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-methods"],"jetpack_featured_media_url":"https:\/\/i0.wp.com\/mindwander.com\/wp-content\/uploads\/2022\/12\/IMG_0437-conv-scaled.jpeg?fit=1920%2C2560&ssl=1","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/mindwander.com\/index.php\/wp-json\/wp\/v2\/posts\/341","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/mindwander.com\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/mindwander.com\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/mindwander.com\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/mindwander.com\/index.php\/wp-json\/wp\/v2\/comments?post=341"}],"version-history":[{"count":0,"href":"https:\/\/mindwander.com\/index.php\/wp-json\/wp\/v2\/posts\/341\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/mindwander.com\/index.php\/wp-json\/wp\/v2\/media\/303"}],"wp:attachment":[{"href":"https:\/\/mindwander.com\/index.php\/wp-json\/wp\/v2\/media?parent=341"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mindwander.com\/index.php\/wp-json\/wp\/v2\/categories?post=341"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mindwander.com\/index.php\/wp-json\/wp\/v2\/tags?post=341"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}