Information pages all in one
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@@ -2,8 +2,6 @@
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using System.Drawing;
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using System.IO;
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using System.Web.Mvc;
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using System.Web.UI.DataVisualization.Charting;
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using System.Web.UI.WebControls;
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namespace LeafWeb.Web.Controllers
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{
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@@ -14,27 +12,7 @@ namespace LeafWeb.Web.Controllers
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return View();
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}
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public ActionResult EDOPublications()
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{
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return View();
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}
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public ActionResult OutputFiles()
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{
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return View();
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}
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public ActionResult Tips()
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{
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return View();
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}
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public ActionResult WhyEDO()
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{
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return View();
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}
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public ActionResult DataRequirements()
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public ActionResult Information()
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{
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return View();
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}
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@@ -1,27 +0,0 @@
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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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@@ -1,14 +0,0 @@
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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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@@ -0,0 +1,98 @@
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<h2>Why EDO?</h2>
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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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<h2>EDO Publications</h2>
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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">
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Reliable estimation of biochemical parameters
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from C3 leaf photosynthesis-intercellular carbon dioxide response curves
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</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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<h2>EDO Data Submission Requirements for C3 Leaves</h2>
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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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<h2>Definitions of Variables in Output Files</h2>
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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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<h2>Tips for Informative A/Ci Measurements</h2>
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<ul>
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<li>
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Relatively densely distributed points in the curvature region
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of an A/Ci curve are crucial for reliable parameter estimation.
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</li>
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<li>
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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.
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</li>
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<li>Identify the Ci range within which the curvature region is located.</li>
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<li>
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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.
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</li>
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<li>Sample the curvature region preferentially.</li>
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</ul>
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@@ -1,23 +0,0 @@
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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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@@ -1,12 +0,0 @@
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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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@@ -1,11 +0,0 @@
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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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@@ -35,19 +35,8 @@
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<li><a href="/LeafCharter">Leaf Charts</a></li>
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</ul>
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</li>
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Information <span class="caret"></span></a>
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<ul class="dropdown-menu">
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<li><a href="/Pages/WhyEDO">Why EDO?</a></li>
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<li><a href="/Pages/EDOPublications">EDO Publications</a></li>
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<li><a href="/Pages/DataRequirements">Submission Requirements</a></li>
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<li><a href="/Pages/OutputFiles">Output Variables</a></li>
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<li><a href="/Pages/Tips">Tips</a></li>
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@* <li role="separator" class="divider"></li>
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<li class="dropdown-header">Nav header</li>
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<li><a href="#">Separated link</a></li>
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<li><a href="#">One more separated link</a></li>*@
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</ul>
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<li>
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<a href="/Pages/Information">Information</a>
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</li>
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</ul>
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@* <ul class="nav navbar-nav navbar-right">
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+1
-5
@@ -948,13 +948,8 @@
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<Content Include="Views\web.config" />
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<Content Include="packages.config" />
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<Content Include="Views\Pages\Index.cshtml" />
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<Content Include="Views\Pages\WhyEDO.cshtml" />
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<Content Include="Views\Pages\EDOPublications.cshtml" />
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<Content Include="Views\Pages\OutputFiles.cshtml" />
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<Content Include="Views\Pages\Tips.cshtml" />
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<Content Include="Views\Shared\_Layout.cshtml" />
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<Content Include="Views\_ViewStart.cshtml" />
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<Content Include="Views\Pages\DataRequirements.cshtml" />
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<Content Include="Scripts\jquery-1.9.1.min.map" />
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<Content Include="Views\LeafCharter\Index.cshtml" />
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<Content Include="Views\LeafInput\Index.cshtml" />
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@@ -980,6 +975,7 @@
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<Content Include="Views\Shared\_ValidationField.cshtml" />
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<Content Include="Views\Shared\EditorTemplates\SelectListViewModel.cshtml" />
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<Content Include="Views\LeafOutput\Index.cshtml" />
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<Content Include="Views\Pages\Information.cshtml" />
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<None Include="Web.Debug.config">
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<DependentUpon>Web.config</DependentUpon>
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</None>
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