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Information pages all in one

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James Kolpack
2016-03-09 11:55:55 -05:00
parent e80ddbc4d6
commit 72caa74bb2
9 changed files with 102 additions and 128 deletions
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Web/Controllers/PagesController.cs
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@@ -2,8 +2,6 @@
using System.Drawing; using System.Drawing;
using System.IO; using System.IO;
using System.Web.Mvc; using System.Web.Mvc;
using System.Web.UI.DataVisualization.Charting;
using System.Web.UI.WebControls;
namespace LeafWeb.Web.Controllers namespace LeafWeb.Web.Controllers
{ {
@@ -14,27 +12,7 @@ namespace LeafWeb.Web.Controllers
return View(); return View();
} }
public ActionResult EDOPublications() public ActionResult Information()
{
return View();
}
public ActionResult OutputFiles()
{
return View();
}
public ActionResult Tips()
{
return View();
}
public ActionResult WhyEDO()
{
return View();
}
public ActionResult DataRequirements()
{ {
return View(); return View();
} }
Web/Views/Pages/DataRequirements.cshtml
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<h1>EDO Data Submission Requirements for C3 Leaves</h1>
<p>
We welcome users to evaluate the EDO approach and strongly encourage users to contribute their
leaf-level measurements towards the development of a global CDIAC leaf database; however, users may
still use the interface without their data becoming part of the larger CDIAC database.
</p>
<p>
To achieve the best possible results and to enhance the utility of your contributions for others,
it is imperative those submitting data provide both the requested core leaf-level variables and
the complementary information necessary to properly qualify the leaf or leaves. The desired core
and companion variables are specified in the sample input file and descriptive "readme" file for each service.
</p>
<p>
The following links provide information on preparing these input files:
</p>
<ul>
<li>
<a title="Describes the required format of the input files" href="/Content/Documents/Readme_InputFile" target="_blank">Readme_InputFile</a>
</li>
<li>
<a title="A sample input file" href="/Content/Documents/SampleInput.csv" target="_blank">Sample Input File</a>
</li>
<li>
<a title="A sample input file to use as a template" href="/Content/Documents/InputFileTemplate.csv" target="_blank">Input File Template</a>
</li>
</ul>
Web/Views/Pages/EDOPublications.cshtml
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<h1>EDO Publications</h1>
<ul>
<li class="pdf">
<a href="/Content/Documents/aci_pce_final.pdf" target="_blank">Reliable estimation of biochemical parameters
from C3 leaf photosynthesis-intercellular carbon dioxide response curves</a>
</li>
<li class="pdf">
<a href="/Content/Documents/response_to_comments_1.pdf" target="_blank">Response to the Subject Editor’s Comments</a>
</li>
<li class="pdf">
<a href="/Content/Documents/response_to_comments_2.pdf" target="_blank">Response to Dr. Graham D. Farquhar’s comments</a>
</li>
</ul>
Web/Views/Pages/Information.cshtml
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<h2>Why EDO?</h2>
<p>
The&nbsp;FvCB model is more complicated than it looks for parameter estimation.&nbsp;
It has several characteristics&nbsp;that invalidate the use of conventional optimization approaches
.&nbsp; For example,&nbsp;the FvCB model is a change-point model and is structurally overparameterized
in individual carboxylation limitation states with respect to A/Ci&nbsp;measurements.&nbsp; Without
recognizing these unique features of the FvCB model, conventional approaches may lead to incorrect
parameters and produce false parameter relatinships.&nbsp;&nbsp;EDO takes into consideration
the&nbsp;unique structure of the FvCB model and is better suited for analysis of A/Ci curves.&nbsp;
For more details, please read Gu et al. (2010).
</p>
<h2>EDO Publications</h2>
<ul>
<li class="pdf">
<a href="/Content/Documents/aci_pce_final.pdf" target="_blank">
Reliable estimation of biochemical parameters
from C3 leaf photosynthesis-intercellular carbon dioxide response curves
</a>
</li>
<li class="pdf">
<a href="/Content/Documents/response_to_comments_1.pdf" target="_blank">Response to the Subject Editor’s Comments</a>
</li>
<li class="pdf">
<a href="/Content/Documents/response_to_comments_2.pdf" target="_blank">Response to Dr. Graham D. Farquhar’s comments</a>
</li>
</ul>
<h2>EDO Data Submission Requirements for C3 Leaves</h2>
<p>
We welcome users to evaluate the EDO approach and strongly encourage users to contribute their
leaf-level measurements towards the development of a global CDIAC leaf database; however, users may
still use the interface without their data becoming part of the larger CDIAC database.
</p>
<p>
To achieve the best possible results and to enhance the utility of your contributions for others,
it is imperative those submitting data provide both the requested core leaf-level variables and
the complementary information necessary to properly qualify the leaf or leaves. The desired core
and companion variables are specified in the sample input file and descriptive "readme" file for each service.
</p>
<p>
The following links provide information on preparing these input files:
</p>
<ul>
<li>
<a title="Describes the required format of the input files" href="/Content/Documents/Readme_InputFile" target="_blank">Readme_InputFile</a>
</li>
<li>
<a title="A sample input file" href="/Content/Documents/SampleInput.csv" target="_blank">Sample Input File</a>
</li>
<li>
<a title="A sample input file to use as a template" href="/Content/Documents/InputFileTemplate.csv" target="_blank">Input File Template</a>
</li>
</ul>
<h2>Definitions of Variables in Output Files</h2>
<p>
LeafWeb employs the Exhaustive Dual Optimization (EDO) approach to fitting A/Ci curves for parameters in the
Farquhar-von Caemmerer-Berry (FvCB) model (Gu et al. 2010). For each A/Ci curve, four sets of parameters are
fitted because a given A/Ci curve might not contain sufficient constraint power for all parameters in the FvCB model.
</p>
<p>
More detailed explanation of the output files are given below:
</p>
<ul>
<li>
<a title="The format of the cntrlbestparameters output file" href="http://leafweb.ornl.gov/Documents/Readme_cntrlbestparameters" target="_blank">Readme_cntrlbestparameters</a>
- This file contains parameters estimated for all A/Ci curves that are submitted in the same batch.
</li>
<li>
<a title="The format of the cntrlcomparison output file" href="http://leafweb.ornl.gov/Documents/Readme_cntrlcomparison" target="_blank">Readme_cntrlcomparison</a>
- This file contains outputs from PISCAL that facilitates examination of how well the fitting was performed.
</li>
<li>
<a title="The format of the cntrlparameters output file" href="http://leafweb.ornl.gov/Documents/Readme_cntrlparameters" target="_blank">Readme_cntrlparameters</a>
- This file is an extended version of the output file 'cntrlbestparameters.csv'
</li>
</ul>
<h2>Tips for Informative A/Ci Measurements</h2>
<ul>
<li>
Relatively densely distributed points&nbsp;in the&nbsp;curvature region
of an A/Ci curve are crucial for reliable&nbsp;parameter estimation.
</li>
<li>
Use data from literature or exploratory measurements to establish the&nbsp;broad
shape&nbsp;of A/Ci curves of similarly positioned leaves of the interested species.
</li>
<li>Identify the Ci range within which&nbsp;the curvature region is located.</li>
<li>
Determine the corresponding cuvette CO<sub>2</sub> range using either prior
knowledge or preliminary measurements.
As an initial try, set the cuvette CO<sub>2</sub> to be 1.5 - 2 times the desired Ci values.
</li>
<li>Sample the curvature region preferentially.</li>
</ul>
Web/Views/Pages/OutputFiles.cshtml
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<h1>Definitions of Variables in Output Files</h1>
<p>
LeafWeb employs the Exhaustive Dual Optimization (EDO) approach to fitting A/Ci curves for parameters in the
Farquhar-von Caemmerer-Berry (FvCB) model (Gu et al. 2010). For each A/Ci curve, four sets of parameters are
fitted because a given A/Ci curve might not contain sufficient constraint power for all parameters in the FvCB model.
</p>
<p>
More detailed explanation of the output files are given below:
</p>
<ul>
<li>
<a title="The format of the cntrlbestparameters output file" href="http://leafweb.ornl.gov/Documents/Readme_cntrlbestparameters" target="_blank">Readme_cntrlbestparameters</a>
- This file contains parameters estimated for all A/Ci curves that are submitted in the same batch.
</li>
<li>
<a title="The format of the cntrlcomparison output file" href="http://leafweb.ornl.gov/Documents/Readme_cntrlcomparison" target="_blank">Readme_cntrlcomparison</a>
- This file contains outputs from PISCAL that facilitates examination of how well the fitting was performed.
</li>
<li>
<a title="The format of the cntrlparameters output file" href="http://leafweb.ornl.gov/Documents/Readme_cntrlparameters" target="_blank">Readme_cntrlparameters</a>
- This file is an extended version of the output file 'cntrlbestparameters.csv'
</li>
</ul>
Web/Views/Pages/Tips.cshtml
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<h1>Tips for Informative A/Ci Measurements</h1>
<ul>
<li>Relatively densely distributed points&nbsp;in the&nbsp;curvature region
of an A/Ci curve are crucial for reliable&nbsp;parameter estimation.</li>
<li>Use data from literature or exploratory measurements to establish the&nbsp;broad
shape&nbsp;of A/Ci curves of similarly positioned leaves of the interested species.</li>
<li>Identify the Ci range within which&nbsp;the curvature region is located.</li>
<li>Determine the corresponding cuvette CO<sub>2</sub> range using either prior
knowledge or preliminary measurements.
As an initial try, set the cuvette CO<sub>2</sub> to be 1.5 - 2 times the desired Ci values.</li>
<li>Sample the curvature region preferentially.</li>
</ul>
Web/Views/Pages/WhyEDO.cshtml
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@@ -1,11 +0,0 @@
<h1>Why EDO?</h1>
<p>
The&nbsp;FvCB model is more complicated than it looks for parameter estimation.&nbsp;
It has several characteristics&nbsp;that invalidate the use of conventional optimization approaches
.&nbsp; For example,&nbsp;the FvCB model is a change-point model and is structurally overparameterized
in individual carboxylation limitation states with respect to A/Ci&nbsp;measurements.&nbsp; Without
recognizing these unique features of the FvCB model, conventional approaches may lead to incorrect
parameters and produce false parameter relatinships.&nbsp;&nbsp;EDO takes into consideration
the&nbsp;unique structure of the FvCB model and is better suited for analysis of A/Ci curves.&nbsp;
For more details, please read Gu et al. (2010).
</p>
Web/Views/Shared/_Layout.cshtml
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<li><a href="/LeafCharter">Leaf Charts</a></li> <li><a href="/LeafCharter">Leaf Charts</a></li>
</ul> </ul>
</li> </li>
<li class="dropdown"> <li>
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Information <span class="caret"></span></a> <a href="/Pages/Information">Information</a>
<ul class="dropdown-menu">
<li><a href="/Pages/WhyEDO">Why EDO?</a></li>
<li><a href="/Pages/EDOPublications">EDO Publications</a></li>
<li><a href="/Pages/DataRequirements">Submission Requirements</a></li>
<li><a href="/Pages/OutputFiles">Output Variables</a></li>
<li><a href="/Pages/Tips">Tips</a></li>
@* <li role="separator" class="divider"></li>
<li class="dropdown-header">Nav header</li>
<li><a href="#">Separated link</a></li>
<li><a href="#">One more separated link</a></li>*@
</ul>
</li> </li>
</ul> </ul>
@* <ul class="nav navbar-nav navbar-right"> @* <ul class="nav navbar-nav navbar-right">
Web/Web.csproj
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<Content Include="Views\web.config" /> <Content Include="Views\web.config" />
<Content Include="packages.config" /> <Content Include="packages.config" />
<Content Include="Views\Pages\Index.cshtml" /> <Content Include="Views\Pages\Index.cshtml" />
<Content Include="Views\Pages\WhyEDO.cshtml" />
<Content Include="Views\Pages\EDOPublications.cshtml" />
<Content Include="Views\Pages\OutputFiles.cshtml" />
<Content Include="Views\Pages\Tips.cshtml" />
<Content Include="Views\Shared\_Layout.cshtml" /> <Content Include="Views\Shared\_Layout.cshtml" />
<Content Include="Views\_ViewStart.cshtml" /> <Content Include="Views\_ViewStart.cshtml" />
<Content Include="Views\Pages\DataRequirements.cshtml" />
<Content Include="Scripts\jquery-1.9.1.min.map" /> <Content Include="Scripts\jquery-1.9.1.min.map" />
<Content Include="Views\LeafCharter\Index.cshtml" /> <Content Include="Views\LeafCharter\Index.cshtml" />
<Content Include="Views\LeafInput\Index.cshtml" /> <Content Include="Views\LeafInput\Index.cshtml" />
@@ -980,6 +975,7 @@
<Content Include="Views\Shared\_ValidationField.cshtml" /> <Content Include="Views\Shared\_ValidationField.cshtml" />
<Content Include="Views\Shared\EditorTemplates\SelectListViewModel.cshtml" /> <Content Include="Views\Shared\EditorTemplates\SelectListViewModel.cshtml" />
<Content Include="Views\LeafOutput\Index.cshtml" /> <Content Include="Views\LeafOutput\Index.cshtml" />
<Content Include="Views\Pages\Information.cshtml" />
<None Include="Web.Debug.config"> <None Include="Web.Debug.config">
<DependentUpon>Web.config</DependentUpon> <DependentUpon>Web.config</DependentUpon>
</None> </None>