Dataset: BIOS-SCOPE survey biogeochemical data
Deployment: AE1712

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/861266

Principal Investigator:

Craig A. Carlson (University of California-Santa Barbara, UCSB)

Co-Principal Investigator:

Stephen Giovannoni (Oregon State University, OSU)

Scientist:

Elisa Halewood (University of California-Santa Barbara, UCSB)

Shuting Liu (University of California-Santa Barbara, UCSB)

BCO-DMO Data Manager:

Dana Stuart Gerlach (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Bermuda Institute of Ocean Sciences Simons Collaboration on Ocean Processes and Ecology (BIOSSCOPE)

Version:

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Description

Methods & Sampling

Dataset acquisition description

Sampling
From July 2016 through July 2019, samples were collected from CTD samplers and Niskin bottles during R/V Atlantic Explorer cruises to understand ocean processes and ecological interactions in the open ocean waters near Bermuda. The BATS program provided monthly collections, while BIOS-SCOPE process cruises provided more detailed information from around-the-clock sampling for the hydrographic variables. Plankton tows were used to assess the temporal and vertical variability of organic and inorganic nutrients, vitamins, metabolites, microbial biomass and production, bacterial and viral DNA, and zooplankton biomass at depths over 1000 meters. In situ sequential filtration pumps collected particles for molecular and isotopic characterization of organic particles that spanned four biologically-relevant size classes over 12 depths. Numerous shipboard experiments were conducted to evaluate zooplankton and microbial respiration, as well as organic matter transformation by bacterioplankton (free living bacteria).

Between February 2017 and September 2018, time series of physical and biogeochemical properties were acquired near the BATS site using three separate Slocum G2 gliders deployed in 10 consecutive missions. Each glider carried a science payload that included a pumped CTD, WetLabs ECOpuck (ChlF and Bp700) and Aanderaa O2 optode, and was programmed to spiral around a 0.5 km box (essentially holding station) and profile between 0 and ~900 meters depth. For five missions the glider was additionally equipped with a Submersible Underwater Nitrate Analyzer (SUNA). Monthly, co-located ship-based CTD and water sample profiles were used to calibrate each of the sensors. These time series demonstrate the relationship between vertical zones, seasons and biogeochemical property distributions.

Analysis
BIOS-SCOPE cruise samples were analyzed at UCSB using the following instruments and methods:

Flow injection analysis was performed on a Lachat QuikChem 8500 series 2 to obtain concentration data for nitrate, nitrite, NO3 + NO2, ortho-phosphate, ammonium, and silicate.

Particulate organic carbon (POC) and particulate organic nitrogen (PON) were measured by combustion analysis using a CEC 440HA elemental analyzer. Additional methodology, calibrations, precision and accuracy, and methodological references are detailed at the UCSB MSI Analytical Lab Website: http://www.msi.ucsb.edu/services/analytical-lab.

Dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) were measured using high temperature catalytic oxidation (HTCO) on a Shimadzu TOC-V system with TNM-1 unit (Carlson et al., 2010).

Bacterioplankton abundance was obtained using Olympus BX51 epifluorescent microscope (Porter & Feig, 1980). Heterotrophic bacterial production was analyzed using 3H-leucine uptake (Smith & Azam, 1992).

Total Dissolved Amino Acids (TDAA) and individual amino acids were measured using HPLC (high performance liquid chromatography) following the methods of Liu et al. (2020). The amino acids include alanine, arginine, aspartic acid, beta-alanine, gamma-aminobutyric acid, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, serine, taurine, threonine, tyrosine, and valine.

Season was derived from the Slocum G2 glider time series data. The glider data had longer deployment periods marking the seasonal changes, so the CTD sampling dates were lined up with the glider data using date/timestamp. Each CTD/bottle profile was assigned a season code based on the alignment with the known seasons and dates from the glider data. Season designations are 1=Mixed, 2=Spring transition, 3=Stratified, 4=Fall transition (for more information, see the Physical Framework document on the Project page)

Slocum G2 glider data. Determined from the glider time series in each year, then each CTD/bottle profile is assigned a season code based on those dates. Season designation. Season = 1 : Mixed 2: Spring transition 3: Stratified 4: Fall transition (see Physical Framework document)

Genomic DNA samples were amplified and sequenced using universal primer sets for 16S and 18S with 'general' Illumina overhang adapters at Center for Genome Research and Biocomputing (Oregon State University) Corvallis, OR. These data have been deposited with links to BioProject accession number PRJNA769790 in the NCBI BioProject database.

*Related dataset with NCBI sequence information and links is (BCO-DMO dataset number TBD)*

Data Processing Description

Dataset Processing Description

Quality Flags:
0=good
1=unknown/below detection limit
4=questionable/high error
8=bad quality/outlier

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Mixed Layer Depth (MLD):

Overview in de Boyer Montegut (2004). The CTD, bottle, and glider profiles are labeled with three definitions of MLD which reflect processes that affect stratification on different time scales:

ML_dens125
- ML_dens125 is defined as the depth where sigma-theta is greater than the surface density by 0.125 kg m-3
- ML_dens125 reflects deepest reach of seasonal convective mixing
- ML_dens125 exhibits LOWEST frequency variability
- ML_dens125 is DEEPEST of three MLD
- refer to Suga et al (2004)

ML_densT2
- ML_densT2 is defined as the depth where sigma-theta exceeds the surface density +0.2*alpha
(where alpha is the thermal expansion coefficient)
- ML_densT2 marks intermediate episodes of convective mixing;
- ML_desnsT2 marks intermediate episodes of convective mixing;
- ML_densT2 exhibits MEDIUM variability
- ML_densT2 has depths between the other two definitions.
- refer to Sprintall & Tomczak (1992)

ML_bvfrq
- ML_bvfrq is defined as the depth where the buoyancy frequency (N2) first exceeds the standard deviation of N2.
- ML_bvfrq responds to diurnal scales of restratification/mixing (and has been adopted by the NAAMES program).
- ML_bvfrq exhibits HIGHEST frequencies
- ML_bvfrq has SHALLOWEST depth
- refer to Mojica & Gaube (in review)

See PhysicalFramework.pdf on Project page for plots comparing these parameters.

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BCO-DMO Processing:

- converted latitude and longitude to decimal degrees (south and west are negative)
- combined date and time columns into a single ISO 8601 formatted datetime
- modified parameter (column) names to conform with BCO-DMO naming conventions
- added conventional header with dataset name, PI name, version date
- missing data identifier "-999" in the original source file was replaced with BCO-DMO default missing data identifier, which varies depending on the type of file that is downloaded from the BCO-DMO data system. For example, missing data will be shown as blank (null) values in the csv files. In MATLAB .mat files it will be displayed as NaN. When viewing data at BCO-DMO the missing value will be shown as "nd" meaning "no data."

More information about this dataset deployment

Funding

Award Number	Funding Source
unknown SCOPE Simons	Simons Foundation

Instruments

Aanderaa Oxygen Optodes

Supplied Name: Aanderaa O2 optode

Supplied Description:

Slocum G2 glider carried a science payload that included Aanderaa oxygen optode.

Instrument Type

Generic Name: Aanderaa Oxygen Optodes

Acronym: AOO

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/351/

Generic Description:

Aanderaa Oxygen Optodes are instrument for monitoring oxygen in the environment. For instrument information see the Aanderaa Oxygen Optodes Product Brochure.

CHN Elemental Analyzer

Supplied Name: CEC 440HA combustion analyzer

Supplied Description:

CEC 440HA combustion analyzer was used to measure particulate organic carbon and particulate organic nitrogen

Instrument Type

Generic Name: CHN Elemental Analyzer

Acronym: CHN_EA

Generic Description:

A CHN Elemental Analyzer is used for the determination of carbon, hydrogen, and nitrogen content in organic and other types of materials, including solids, liquids, volatile, and viscous samples.

CTD Sea-Bird SBE 911plus

Supplied Name: CTD SeaBird 911+

Supplied Description:

CTD SeaBird 911+ was deployed to measure temperature, conductivity, salinity, pressure, oxygen, and fluorescence.

Instrument Type

Generic Name: CTD Sea-Bird SBE 911plus

Acronym: CTD SBE 911plus

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/

Generic Description:

The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics

Flow Injection Analyzer

Supplied Name: Lachat QuikChem 8500 series 2

Supplied Description:

Lachat QuikChem 8500 series 2 was used to measure nitrate, nitrite, ortho-phosphate, ammonium, and silicate by flow injection analysis

Instrument Type

Generic Name: Flow Injection Analyzer

Acronym: FIA

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB36/

Generic Description:

An instrument that performs flow injection analysis. Flow injection analysis (FIA) is an approach to chemical analysis that is accomplished by injecting a plug of sample into a flowing carrier stream. FIA is an automated method in which a sample is injected into a continuous flow of a carrier solution that mixes with other continuously flowing solutions before reaching a detector. Precision is dramatically increased when FIA is used instead of manual injections and as a result very specific FIA systems have been developed for a wide array of analytical techniques.

Fluorescence Microscope

Supplied Name: Olympus BX51 epifluorescent microscope

Supplied Description:

Olympus BX51 epifluorescent microscope was used to obtain bacterioplankton abundance in 10^8 cells per kilogram.

Instrument Type

Generic Name: Fluorescence Microscope

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/

Generic Description:

Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.

MOCNESS

Supplied Description:

Mesozooplankton sampling will be carried out seasonally via a Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) equipped with 200 µm nets during the mid-day and mid-evening.

Instrument Type

Generic Name: MOCNESS

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/

Generic Description:

The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. There are currently 8 different sizes of MOCNESS in existence which are designed for capture of different size ranges of zooplankton and micro-nekton Each system is designated according to the size of the net mouth opening and in two cases, the number of nets it carries. The original MOCNESS (Wiebe et al, 1976) was a redesigned and improved version of a system described by Frost and McCrone (1974).(from MOCNESS manual) This designation is used when the specific type of MOCNESS (number and size of nets) was not specified by the contributing investigator.

Niskin bottle

Supplied Name: Niskin bottles

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Nutrient Autoanalyzer

Supplied Name: Submersible Underwater Nitrate Analyzer (SUNA)

Supplied Description:

For five missions the glider was additionally equipped with a Submersible Underwater Nitrate Analyzer (SUNA)

Instrument Type

Generic Name: Nutrient Autoanalyzer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/

Generic Description:

Nutrient Autoanalyzer is a generic term used when specific type, make and model were not specified. In general, a Nutrient Autoanalyzer is an automated flow-thru system for doing nutrient analysis (nitrate, ammonium, orthophosphate, and silicate) on seawater samples.

Reeve Net

Supplied Name: Reeve net

Supplied Description:

During the winter and the summer cruises a Reeve net (1 m mouth, 150 µm mesh) will be towed obliquely from 150 m to the surface at the start of each evening when the echo-sounder indicates that the DVM zooplankton have returned to the surface, and late evening (~ 4 am) prior to the descent of the DVM layer.

Instrument Type

Generic Name: Reeve Net

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/NETT0147/

Generic Description:

A Reeve Net is a conventional ring net with a very large acrylic cylindrical cod-end (30 liters) designed to collect fragile gelatinous animals. The net is lowered to a particular depth and then hauled slowly back to the surface (5-10 m/min). Reeve (1981) also described a double net system with no bridle and flotation at the net mouth that is attached to a roller mechanism that rides on a tow wire.
The roller system is locked in place by a pressure release device. Once below a set pressure, the roller
and nets are released and they float slowly up the wire, gently collecting the zooplankton, without being
influenced by the motion of the vessel and associated vertical wire movements. (from Wiebe and Benfield, 2003)

Shimadzu TOC-V Analyzer

Supplied Name: Shimadzu TOC-V

Supplied Description:

High temperature catalytic oxidation (HTCO) was performed on a Shimadzu TOC-V system with TNM-1 chemiluminescent detector assembly

Instrument Type

Generic Name: Shimadzu TOC-V Analyzer

Acronym: Shimadzu TOC-V

Community Identifier: http://onto.nerc.ac.uk/CAST/124

Generic Description:

A Shimadzu TOC-V Analyzer measures DOC by high temperature combustion method.

Slocum G2 glider

Supplied Description:

Time series of physical and biogeochemical properties were acquired near the BATS site using three separate Slocum G2 gliders

Instrument Type

Generic Name: Slocum G2 glider

Acronym: Slocum G2

Generic Description:

A long-range autonomous underwater vehicle (AUV) based on buoyancy. It is used for remote water column sampling. It uses hydraulic buoyancy change to alter the vehicle density in relation to the surrounding water thereby causing the vehicle to either float or sink. Given an appropriate dive or climb angle, the wings and body lift and convert some of this vertical motion into a forward saw tooth horizontal motion. Periodically, the glider surfaces and calls via Iridium Satellite Phone (anywhere in world) or Free Wave RF Modem (line of sight) in to Dockserver (auto attendant computer) to relay navigational fix, data and receive further instructions for command and control. The glider is capable of storm sampling and can be flown in a coordinated fleet. It is 1.5 m in length, has a hull diameter of 22 cm and mass of 54 kgs. It has an exchangeable payload (capacity up to 6 L) which is capable of housing a variety of environmental sensors such as nitrate and oxygen. It uses lithium or alkaline batteries. It has a deployment range of 600-6000 km, a deployment length of 15 days to 12 months and an operating depth range of 4-1000m. Navigation is via GPS waypoints, a pressure and altimeter sensor. Maximum speed is .35 m/s. It transmits via RF modem, Iridium (RUDICS), ARGOS or acoustic modem.

Total Nitrogen Analyzer

Supplied Name: TNM-1 chemiluminescent detector assembly

Supplied Description:

High temperature catalytic oxidation (HTCO) was performed on a Shimadzu TOC-V system with TNM-1 chemiluminescent detector assembly that permits Total Nitrogen measurements.

Instrument Type

Generic Name: Total Nitrogen Analyzer

Acronym: TN analyzer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/

Generic Description:

A unit that accurately determines the nitrogen concentrations of organic compounds typically by detecting and measuring its combustion product (NO). See description document at: http://bcodata.whoi.edu/LaurentianGreatLakes_Chemistry/totalnit.pdf

Wet Labs ECO Puck

Supplied Name: WetLabs ECOpuck (ChlF and Bp700)

Supplied Description:

Slocum G2 glider carried a science payload that included WetLabs ECOpuck (ChlF and Bp700)

Instrument Type

Generic Name: Wet Labs ECO Puck

Generic Description:

The Puck is a miniature version of the ECO series of sensors, specifically designed for use in AUVs, profiling floats, and Slocum gliders with a dry science bay. This compact optical sensor is available in combinations of backscattering and fluorescence measurements.
Manufacturer's website: https://www.seabird.com/auv-rov-sensors/eco-puck/family?productCategoryId=55352274651

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Program	Program name	unitless	project
Cruise_ID	Vessel and cruise number	unitless	cruise_id
Cast	Cast number according to CTD log sheets	unitless	cast
Niskin	Niskin bottle number according to CTD log sheets	unitless	bot_Nis
decy	Date in decimal year	decimal years	year_decimal
ISO_DateTime_UTC	Date and UTC Time in ISO8601 format	unitless	ISO_DateTime_UTC
Latitude	Latitude at start of cast	decimal degrees	lat
Longitude	Longitude at start of cast (West is negative)	decimal degrees	lon
Depth	CTD bottle collection depth	meters (m)	depth
Nominal_Depth	Target depth	meters (m)	depth
Temp	Standard CTD temperature profiling	degrees Celsius	temp
CTD_SBE35T	Temperature from SeaBird 35 CTD which has 8 second average taken at time of the bottle fire. This sensor has an accuracy of 0.0001C as compared to the standard profiling units which have an accuracy of 0.002C.	degrees Celsius	temp2
Conductivity	Conductivity	Siemens per meter (S/m)	cond
CTD_S	Salinity measured by CTD	practical salinity units (PSU)	sal_ctd
Pressure	Pressure	decibars (dbar)	press
sig_theta	Sigma-theta	kilograms per cubed meter (kg/m^3)	sigma_0
O2	CTD Oxygen	micromole per kilogram (umol/kg)	O2
BAC	Beam attenuation coefficient	per meter	beam_cp
Fluo	CTD Fluorescence	microgram per liter (ug/L)	fluor
PAR	CTD Photosynthetically active radiation	microEinsteins per second per square meter (uE/m^2/sec)	PAR
Pot_Temp	Potential temperature	degrees Celsius	potemp
Niskin_temp	modeled Niskin temperature when it gets back on deck	degrees Celsius	temp
NO3_plus_NO2	Nitrate plus nitrite concentration	micromole per kilogram (umol/kg)	NO3_NO2
NO3_plus_NO2_QF	Nitrate plus nitrite quality flag	unitless	q_flag
NO3	Nitrate concentration	micromole per kilogram (umol/kg)	NO3
NO3_QF	Nitrate quality flag	unitless	q_flag
NO2	Nitrite concentration	micromole per kilogram (umol/kg)	NO2
NO2_QF	Nitrite quality flag	unitless	q_flag
PO4	Ortho-phosphate concentration	micromole per kilogram (umol/kg)	PO43-
PO4_QF	Ortho-phosphate quality flag	unitless	q_flag
NH4	Ammonium concentration	micromole per kilogram (umol/kg)	NH4
NH4_QF	Ammonium quality flag	unitless	q_flag
SiO2	Silicate concentration	micromole per kilogram (umol/kg)	SiO2
SiO2_QF	Silicate quality flag	unitless	q_flag
POC	Particulate organic carbon	micrograms per kilogram (ug/kg)	POC
POC_QF	Particulate organic carbon quality flag	unitless	q_flag
PON	Particulate organic nitrogen	micrograms per kilogram (ug/kg)	PON
PON_QF	Particulate organic nitrogen quality flag	unitless	q_flag
DOC	Dissolved organic carbon concentration	micromole per kilogram (umol/kg)	DOC
DOC_QF	Dissolved organic carbon quality flag	unitless	q_flag
TDN	Total dissolved nitrogen concentration	micromole per kilogram (umol/kg)	TDN
TDN_QF	Total dissolved nitrogen quality flag	unitless	q_flag
Bact	Bacterioplankton abundance from microscopy with DAPI stain	cells times 100 million per kilogram (cells*10^8/kg)	bact_abund
Bact_QF	Bacterioplankton abundance quality flag	unitless	q_flag
BP_Leu	Heterotrophic bacterial production based on 3H leucine incorporation	picomole per liter per hour (pmol/L/hr)	bact_prod
BP_Leu_QF	Bacterial production quality flag	unitless	q_flag
TDAA	Total dissolved amino acid	nanomole per liter (nmol/L)	amino_conc
TDAA_QF	Total dissolved amino acid quality flag	unitless	q_flag
Ala	Amino acid alanine concentration	nanomole per liter (nmol/L)	amino_conc
Arg	Amino acid arginine concentration	nanomole per liter (nmol/L)	amino_conc
Asp	Amino acid aspartic acid concentration	nanomole per liter (nmol/L)	amino_conc
Beta_Ala	Amino acid beta-alanine concentration	nanomole per liter (nmol/L)	amino_conc
GABA	Amino acid gamma-aminobutyric acid concentration	nanomole per liter (nmol/L)	amino_conc
Glu	Amino acid glutamic acid concentration	nanomole per liter (nmol/L)	amino_conc
Gly	Amino acid glycine concentration	nanomole per liter (nmol/L)	amino_conc
His	Amino acid histidine concentration	nanomole per liter (nmol/L)	amino_conc
Ile	Amino acid isoleucine concentration	nanomole per liter (nmol/L)	amino_conc
Leu	Amino acid leucine concentration	nanomole per liter (nmol/L)	amino_conc
Lys	Amino acid lysine concentration	nanomole per liter (nmol/L)	amino_conc
Met	Amino acid methionine concentration	nanomole per liter (nmol/L)	amino_conc
Phe	Amino acid phenylalanine concentration	nanomole per liter (nmol/L)	amino_conc
Ser	Amino acid serine concentration	nanomole per liter (nmol/L)	amino_conc
Tau	Amino acid derivative taurine concentration	nanomole per liter (nmol/L)	amino_conc
Thr	Amino acid threonine concentration	nanomole per liter (nmol/L)	amino_conc
Tyr	Amino acid tyrosine concentration	nanomole per liter (nmol/L)	amino_conc
Val	Amino acid valine concentration	nanomole per liter (nmol/L)	amino_conc
V1V2_ID	Sequence ID for 16S amplicon V1V2 region	unitless	sample
V4_18s_ID	Sequence ID for 18S V4 region	unitless	sample
Sunrise	Time of sunrise in UTC derived from CTD data and computed from geographic position and date	unitless	time
Sunset	Time of sunset in UTC derived from CTD data and computed from geographic position and date	unitless	time
MLD_dens125	Mixed layer depth defined by surface density plus 0.125 kilograms per cubed meter (see Acquisition description)	meters (m)	depth_mixed_layer
MLD_bvfrq	Depth of "active mixing" defined by buoyancy frequency after Mojica & Gaube (see Acquisition description)	meters (m)	depth_mixed_layer
MLD_densT2	MLD from Thermal Expansion Coeff, and dT=0.2 deg C (see Acqusition description)	meters (m)	depth_mixed_layer
DCM	Depth of chlorophyll maximum (from CTD fluorometer)	meters (m)	depth
VertZone	Vertical Zone designation where vertical layers 0 to 10 are defined by dynamical and biogeochemical criteria (see Table 1 under Supplemental Files)	unitless	depth_comment
Season	Season designation where 1=Mixed, 2=Spring Transition, 3=Stratified, 4=Fall Transition	unitless	season

Database

Contribute Data

Dataset: BIOS-SCOPE survey biogeochemical data
Deployment: AE1712

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: BIOS-SCOPE survey biogeochemical dataDeployment: AE1712

Dataset acquisition description

Dataset Processing Description

Dataset: BIOS-SCOPE survey biogeochemical data
Deployment: AE1712