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Course Materials

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Related Files

» UNABRIDGED COURSE SYLLABUS (505 PAGES, 17-18 MB)

» At-A-Glance Course Schedule

» Detailed Course Schedule

» OA Short Course Participant Learning Outcomes

» Chris Sabine: Overview of the Ocean CO2 System

» Andrew Dickson: Introduction to CO2 Chemistry in Seawater Media

» Aleck Wang: Introduction to Underway pCO2 System

» Short reference card for R

» seacarb training

» seacarb test data

» Andrew Dickson: pH and Alkalinity

» Dave Hutchins: Overview of Biogeochemical Feedbacks

» IRGA DIC Results

» Coulometric DIC movie

» Andrew Dickson: Quality Control of Analytical Measurements of CO2 Parameters

» Andrew Dickson: Implications of Uncertainties in Equilibrium Constants and Analytical Measurements

» Chris Sabine: Choosing the Optimal Parameters for a Particular Ocean Acidification Experiment and Learning How Well You Need to Measure the Parameters You Choose

» Chris Langdon: Overview of Experimental Design

» Jeanne-Pierre Gattuso: Approaches, Tools to Manipulate Carbonate Chemistry

» Shi et al. (2009)
Shi, D., Xu, Y., and Morel, F. M. M. (2009). Effects of the pH/pCO2 control method on medium chemistry and phytoplankton growth, Biogeosciences 6: 1199-1207.

» Kim Yates: Hands-on CO2SYS exercise

» Sabine/Dickson: Summary of discussion on optimal CO2 parameters

» Debora Iglesias-Rodriguez: Algal Culturing Overview

» de Beer et al. (2000)
de Beer D., Kühl M., Stambler N., Vaki L. (2000) A microsensor study of light enhanced Ca2+ uptake and photosynthesis in the reef-building hermatypic coral Favia sp. Marine Ecology Progress Series 194, 75–85.

» Al-Horani et al. (2003)
Al-Horani, F.A., Al-Moghrabi, S.M., de Beer, D. (2003). The mechanism of calcification and its relation to photosynthesis and respiration in the scleractinian coral Galaxea fascicularis.  Marine Biology 142: 419-426.

» Al-Horani et al. (2007)
Al-Horani, F.A., Tambutté, É., Allemand, D. (2007). Dark calcification and the daily rhythm of calcification in the scleractinian coral, Galaxea fascicularis. Coral Reefs 26: 531–538.

» de Nooijer et al. (2009)
de Nooijer L.J., Takashi Toyofuku T., Kitazato H. (2009). Foraminifera promote calcification by elevating their intracellular pH. PNAS 106: www.pnas.org/cgi/doi/10.1073/pnas.0904306106.

» Whitman Miller: Measuring Calcification in Biological Experiments - Mollusks

» William Balch: Radioisotope Techniques for measuring coccolithophore calcification

» Debora Iglesias-Rodriguez: DIR-PIC measurements for estimating calcification

» Andersson et al. (2008)
Andersson, A.J., Mackenzie, F.T., Bates, N.T. (2008). Life on the margin: implications of ocean acidification on Mg-calcite, high latitude and cold-water marine calcifiers. Marine Ecology Progress Series 373: 265-273.

» Morse et al. (2006)
Morse, J.W., Andersson, A.J., Mackenzie, F.T. (2006). Initial responses of carbonate-rich shelf sediments to rising atmospheric pCO2 and “ocean acidification”: Role of high Mg-calcites. Geochimica et Cosmochimica Acta 70: 5814-5830.

» Chris Langdon: Measuring calcification in the field

» Reiner Schlitzer: Ocean Data View

» Scott Doney: Biogeochemical Modelling Introduction

» Brad Seibel: Physiology

» Seibel et al. (In Press) critique of Brewer & Peltzer respiration index

» Bob Key (given by S. Doney): Large Data Sets

» Data from coral calcification experiment

» Data from larval mollusk experiment

» Cyndy Chandler: Introduction to Data Management

» Cyndy Chandler: Shipboard Practices for Data Management

» Anne-Marin Nisumaa: Data rescue presentation

» Scott Doney: Biogeochemical Modeling Part II

» Michael Holcomb: Experimental Wrap-up

» Chris Langdon: Experimental Wrap-up

» Chris DuFore: Spectrophotometric TA spreadsheet

» Chris DuFore: Spectrophotometric pH spreadsheet

» Alex Kozyr: Data Reporting

» Group Photo: By Mark Carls

» Schuster et al. (2009) dissolved carbon instrumentation paper

» euler_demo.m

» dicbio.m

» equic.m

» pco2_dicalk.m

» dicbio_main.m

» OA course TA and pCO2 equilibrator comparisons

Related Links

» Guide for Best Practices on Ocean Acidification Research and Data Reporting

Video Footage of Course Lectures
Click on the right for accompanying lectures (in pdf format) and other reference material from the course. The video files are being processed and will be posted as they become available.

MONDAY NOVEMBER 2
TUESDAY NOVEMBER 3
WEDNESDAY NOVEMBER 4
THURSDAY NOVEMBER 5
 FRIDAY NOVEMBER 6
SATURDAY NOVEMBER 7
MONDAY NOVEMBER 9
TUESDAY NOVEMBER 10
WEDNESDAY NOVEMBER 11
THURSDAY NOVEMBER 12
FRIDAY NOVEMBER 13

Information on CO2 Instrumentation
International Ocean Carbon Coordination Project (IOCCP) website (click on Sensors in lefthand menu) - includes instrumentation information for measuring dissolved inorganic carbon (DIC), pH, total alkalinity, pCO2, and particulate carbon

REQUIRED SOFTWARE

CO2SYS (Sabine)

CO2SYS_calc_XLS: Pierrot, D. E. Lewis,and D. W. R. Wallace. 2006. MS Excel Program Developed for CO2 System Calculations. ORNL/CDIAC-105a. Carbon Dioxide Information Analysis Center, Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee.

SEACARB (Gattuso)

The software package seacarb will be used during the course. All participants are invited to download and install, before the course starts, the following software on their laptop:

1) The version of the R program suitable with the OS installed on your laptop. Versions for Mac OSX, linux, unix and Windows are available here.

2) The R package seacarb. To do that, launch R, go to "Packages & Data:Packages installer", click on "Get list", look for seacarb and click "Install selected".

3) seacarb manual


BIOGEOCHEMICAL MODELING
MIT/WHOI Modeling Course  (Doney)

Carbon Dioxide Information Analysis Center (CDIAC)  (Key)

What We Know About Climate Change (Boston Review Books) by Kerry Emanuel, Judith
A. Layzer, and William R. Moomaw (Hardcover - Sep 30, 2007), The MIT Press, 96 pp.,
Language: English, ISBN-10: 0262050897, ISBN-13: 978-0262050890.

Easterling, D. R., and M. F. Wehner (2009), Is the climate warming or cooling?, Geophys. Res. Lett., 36, L08706, http://www.agu.org/journals/gl/gl0908/2009GL037810/doi:10.1029/2009GL037810.

November 11 Biogeochemical Modeling Demonstration (Doney): Matlab Scripts (download matlab files to the right)



OCEAN DATA VIEW (Schlitzer)

Download ODV 4.2.0. Choose the version for your computer (Windows, Mac OS X or Linux) and follow the installation instructions. People need to register to get access.

Download the CARINA data and follow installation instructions.

Download the GLODAP data and follow installation instructions.

Participants new to ODV are strongly encouraged to try running ODV on the CARINA and GLODAP datasets before they come to the course. The getting started document and the ODV User's Guide should help you get acquainted with the software. Context-sensitive help is available from inside ODV. Participants are also strongly encouraged to bring their own data. Practicing the import of new data into ODV will be part of the course.


DATA MANAGEMENT AND REPORTING (Chandler/Kozyr)

Important Data Management Links (Chandler)

Important Data Reporting Links (Kozyr)

CDIAC Global Ocean CO2 Database Components



IMPORTANT BACKGROUND MATERIALS: SEGMENTS 1 & 2

Riebesell, U., Fabry, V. J., Gattuso, J-P (Eds.) (In Preparation). Guide to Best Practices in Ocean Acidification Research and Data Reporting.

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. 



Last updated: June 15, 2016