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<h1>EDO Data Submission Requirements for C3 Leaves</h1>
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<p>
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We welcome users to evaluate the EDO approach and strongly encourage users to contribute their
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leaf-level measurements towards the development of a global CDIAC leaf database; however, users may
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still use the interface without their data becoming part of the larger CDIAC database.
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</p>
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<p>
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To achieve the best possible results and to enhance the utility of your contributions for others,
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it is imperative those submitting data provide both the requested core leaf-level variables and
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the complementary information necessary to properly qualify the leaf or leaves. The desired core
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and companion variables are specified in the sample input file and descriptive "readme" file for each service.
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</p>
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<p>
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The following links provide information on preparing these input files:
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</p>
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<ul>
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<li>
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<a title="Describes the required format of the input files" href="/Content/Documents/Readme_InputFile" target="_blank">Readme_InputFile</a>
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</li>
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<li>
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<a title="A sample input file" href="/Content/Documents/SampleInput.csv" target="_blank">Sample Input File</a>
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</li>
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<li>
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<a title="A sample input file to use as a template" href="/Content/Documents/InputFileTemplate.csv" target="_blank">Input File Template</a>
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</li>
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</ul>
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<h1>EDO Publications</h1>
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<ul>
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<li class="pdf">
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<a href="/Content/Documents/aci_pce_final.pdf" target="_blank">Reliable estimation of biochemical parameters
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from C3 leaf photosynthesis-intercellular carbon dioxide response curves</a>
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</li>
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<li class="pdf">
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<a href="/Content/Documents/response_to_comments_1.pdf" target="_blank">Response to the Subject Editor’s Comments</a>
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</li>
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<li class="pdf">
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<a href="/Content/Documents/response_to_comments_2.pdf" target="_blank">Response to Dr. Graham D. Farquhar’s comments</a>
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</li>
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</ul>
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<h1>Welcome to LeafWeb</h1>
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<p>
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<strong>Mission: </strong>LeafWeb is a SErvice-in-Exchange-for-Data-Sharing (SEEDS) Project.
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The objective is to develop a global database of biochemical, physiological, and biophysical properties of
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single leaves to support studies of plant functions and terrestrial carbon cycle modeling.
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LeafWeb provides automated numerical analyses of leaf gas exchange measurements. With the approval of the user,
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the data LeafWeb receives are preserved and captured. This effort is part of ongoing research and data management
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activities in the area of climate change science at Oak Ridge National Laboratory.
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</p>
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<p>
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<strong>Make your data count:</strong> As investigators use LeafWeb and contribute their data,
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the resulting "global leaf database" will grow and be freely available from the
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<a href="http://cdiac.ornl.gov/" target="_blank">Carbon Dioxide Information Analysis Center</a> (CDIAC).
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The value of a particular set of leaf gas exchange measurements depends largely on supporting information about the leaf or leaves.
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It is crucial to provide not just the gas exchange data but also complementary information necessary to interpret the data and put the leaf in context.
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</p>
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<p>
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<strong>Analysis of leaf gas exchange measurements:</strong> The analysis involves fitting the
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Farquhar-von Caemmerer-Berry (FvCB) model to the data for C3 plants with the newly developed
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Exhaustive Dual Optimization (EDO) approach developed by <a href="/Content/Documents/aci_pce_final.pdf" target="_blank">Gu et al.</a> (2010).
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Analysis capabilities for C4 plants are being developed. Users will be notified by e-mail when their anlysis results are available from the LeafWeb site.
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</p>
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<h2>Submitting Data and Retrieving Results</h2>
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<ul>
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<li><a href="/LeafInput">C3 Photosynthesis</a> (Click to enter)</li>
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<li>C4 Photosynthesis (under development)</li>
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</ul>
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<h1>Definitions of Variables in Output Files</h1>
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<p>
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LeafWeb employs the Exhaustive Dual Optimization (EDO) approach to fitting A/Ci curves for parameters in the
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Farquhar-von Caemmerer-Berry (FvCB) model (Gu et al. 2010). For each A/Ci curve, four sets of parameters are
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fitted because a given A/Ci curve might not contain sufficient constraint power for all parameters in the FvCB model.
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</p>
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<p>
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More detailed explanation of the output files are given below:
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</p>
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<ul>
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<li>
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<a title="The format of the cntrlbestparameters output file" href="http://leafweb.ornl.gov/Documents/Readme_cntrlbestparameters" target="_blank">Readme_cntrlbestparameters</a>
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- This file contains parameters estimated for all A/Ci curves that are submitted in the same batch.
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</li>
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<li>
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<a title="The format of the cntrlcomparison output file" href="http://leafweb.ornl.gov/Documents/Readme_cntrlcomparison" target="_blank">Readme_cntrlcomparison</a>
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- This file contains outputs from PISCAL that facilitates examination of how well the fitting was performed.
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</li>
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<li>
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<a title="The format of the cntrlparameters output file" href="http://leafweb.ornl.gov/Documents/Readme_cntrlparameters" target="_blank">Readme_cntrlparameters</a>
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- This file is an extended version of the output file 'cntrlbestparameters.csv'
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</li>
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</ul>
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<h1>Tips for Informative A/Ci Measurements</h1>
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<ul>
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<li>Relatively densely distributed points in the curvature region
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of an A/Ci curve are crucial for reliable parameter estimation.</li>
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<li>Use data from literature or exploratory measurements to establish the broad
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shape of A/Ci curves of similarly positioned leaves of the interested species.</li>
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<li>Identify the Ci range within which the curvature region is located.</li>
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<li>Determine the corresponding cuvette CO<sub>2</sub> range using either prior
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knowledge or preliminary measurements.
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As an initial try, set the cuvette CO<sub>2</sub> to be 1.5 - 2 times the desired Ci values.</li>
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<li>Sample the curvature region preferentially.</li>
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</ul>
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<h1>Why EDO?</h1>
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<p>
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The FvCB model is more complicated than it looks for parameter estimation.
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It has several characteristics that invalidate the use of conventional optimization approaches
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. For example, the FvCB model is a change-point model and is structurally overparameterized
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in individual carboxylation limitation states with respect to A/Ci measurements. Without
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recognizing these unique features of the FvCB model, conventional approaches may lead to incorrect
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parameters and produce false parameter relatinships. EDO takes into consideration
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the unique structure of the FvCB model and is better suited for analysis of A/Ci curves.
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For more details, please read Gu et al. (2010).
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</p>
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