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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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<!DOCTYPE html>
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<html>
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<head>
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<title>Mileage Traker - ETHRA - @ViewBag.Title</title>
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<meta name="viewport" content="width=device-width, initial-scale=1.0"/>
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<link href="@Url.Content("~/Content/bootstrap.min.css")" rel="stylesheet" type="text/css" />
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<link href="@Url.Content("~/Content/bootstrap-responsive.min.css")" rel="stylesheet" type="text/css" />
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<link href="@Url.Content("~/Content/LeafWeb.css")" rel="stylesheet" type="text/css" />
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@RenderSection("Styles", false)
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</head>
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<body>
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@* <noscript>
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This site requires JavaScript.
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Here are the <a href="http://www.enable-javascript.com/" target="_blank">
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instructions how to enable JavaScript in your web browser</a>.
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</noscript>*@
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<header>
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<nav class="navbar navbar-default navbar-static-top">
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<div class="container">
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<div class="navbar-header">
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar">
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<span class="sr-only">Toggle navigation</span>
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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</button>
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<a class="navbar-brand" href="/">LeafWeb</a>
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</div>
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@*http://stackoverflow.com/questions/20410623/how-to-add-active-class-to-html-actionlink-in-asp-net-mvc*@
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<div id="navbar" class="navbar-collapse collapse">
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<ul class="nav navbar-nav">
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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">Leaf Data <span class="caret"></span></a>
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<ul class="dropdown-menu">
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<li><a href="#">Leaf Input</a></li>
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<li><a href="#">Leaf Output</a></li>
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<li><a href="#">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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</ul>
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@* <ul class="nav navbar-nav navbar-right">
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<li><a href="../navbar/">Default</a></li>
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<li class="active"><a href="./">Static top <span class="sr-only">(current)</span></a></li>
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<li><a href="../navbar-fixed-top/">Fixed top</a></li>
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</ul>*@
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</div>
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<!--/.nav-collapse -->
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</div>
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</nav>
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</header>
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<div id="content" class="container-fluid">
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@RenderBody()
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</div>
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<footer>
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LeafWeb © 2015 ORNL
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</footer>
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<script src="@Url.Content("~/Scripts/jquery-1.9.1.min.js")" type="text/javascript"></script>
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<script src="@Url.Content("~/Scripts/bootstrap.min.js")" type="text/javascript"></script>
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@RenderSection("Scripts", false)
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</body>
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</html>
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@{
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Layout = "~/Views/Shared/_Layout.cshtml";
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}
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<?xml version="1.0"?>
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<configuration>
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<configSections>
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<sectionGroup name="system.web.webPages.razor" type="System.Web.WebPages.Razor.Configuration.RazorWebSectionGroup, System.Web.WebPages.Razor, Version=3.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35">
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<section name="host" type="System.Web.WebPages.Razor.Configuration.HostSection, System.Web.WebPages.Razor, Version=3.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" requirePermission="false" />
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<section name="pages" type="System.Web.WebPages.Razor.Configuration.RazorPagesSection, System.Web.WebPages.Razor, Version=3.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" requirePermission="false" />
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</sectionGroup>
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</configSections>
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<system.web.webPages.razor>
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<host factoryType="System.Web.Mvc.MvcWebRazorHostFactory, System.Web.Mvc, Version=5.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
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<pages pageBaseType="System.Web.Mvc.WebViewPage">
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<namespaces>
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<add namespace="System.Web.Mvc" />
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<add namespace="System.Web.Mvc.Ajax" />
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<add namespace="System.Web.Mvc.Html" />
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<add namespace="System.Web.Routing" />
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<add namespace="Web" />
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</namespaces>
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</pages>
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</system.web.webPages.razor>
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<appSettings>
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<add key="webpages:Enabled" value="false" />
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</appSettings>
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<system.webServer>
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<handlers>
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<remove name="BlockViewHandler"/>
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<add name="BlockViewHandler" path="*" verb="*" preCondition="integratedMode" type="System.Web.HttpNotFoundHandler" />
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</handlers>
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</system.webServer>
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</configuration>
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