build based on 9e38446

dev/Bachmann/index.html

@@ -34,4 +34,4 @@
 @printf("First element in the gradient = %.2e\n", gradient[1])
 @printf(&quot;First element in the Gauss-Newton Hessian = %.2f\n&quot;, hessian[1, 1])</code></pre><pre><code class="nohighlight hljs">Cost for Bachmann = -418.41
 First element in the gradient = -1.85e-03
-First element in the Gauss-Newton Hessian = 584.10</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Brannmark/">« Models with pre-equilibration (steady-state simulation)</a><a class="docs-footer-nextpage" href="../Beer/">Models with many conditions specific parameters »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 14 August 2023 17:52">Monday 14 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+First element in the Gauss-Newton Hessian = 584.10</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Brannmark/">« Models with pre-equilibration (steady-state simulation)</a><a class="docs-footer-nextpage" href="../Beer/">Models with many conditions specific parameters »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 14 August 2023 20:30">Monday 14 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/Beer/index.html

@@ -21,4 +21,4 @@
 @printf("First element in the gradient = %.2e\n", gradient[1])
 @printf(&quot;First element in the hessian = %.2f\n&quot;, hessian[1, 1])</code></pre><pre><code class="nohighlight hljs">Cost = -58622.91
 First element in the gradient = 7.17e-02
-First element in the hessian = 755266.33</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Bachmann/">« Medium sized models and adjoint sensitivity analysis</a><a class="docs-footer-nextpage" href="../Beer_julia_import/">Providing the model as a Julia file instead of an SBML File »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 14 August 2023 17:52">Monday 14 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+First element in the hessian = 755266.33</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Bachmann/">« Medium sized models and adjoint sensitivity analysis</a><a class="docs-footer-nextpage" href="../Beer_julia_import/">Providing the model as a Julia file instead of an SBML File »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 14 August 2023 20:30">Monday 14 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/Beer_julia_import/index.html

@@ -52,4 +52,4 @@
 pathYaml = joinpath(@__DIR__, "Beer", "Beer_MolBioSystems2014.yaml") 
 pathJuliaFile = joinpath(@__DIR__, "Beer", "Julia_import_files", "Beer_Julia_Import.jl")
 petabModel = readPEtabModel(pathYaml, verbose=true, jlFilePath=pathJuliaFile)</code></pre><pre><code class="nohighlight hljs">PEtabModel for model Beer. ODE-system has 4 states and 9 parameters.
-Generated Julia files are at ...</code></pre><p>Moving forward, you can use the imported model similar to any other model imported from an SBML-file. To get an idea of how to use the wpetabModel` to compute the cost, gradient or hessian for an ODE parameter estimation problem, please refer to the tutorial for the <a href="../Beer/#Beer_tut">Beer model</a>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Beer/">« Models with many conditions specific parameters</a><a class="docs-footer-nextpage" href="../Parameter_estimation/">Parameter estimation »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 14 August 2023 17:52">Monday 14 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+Generated Julia files are at ...</code></pre><p>Moving forward, you can use the imported model similar to any other model imported from an SBML-file. To get an idea of how to use the wpetabModel` to compute the cost, gradient or hessian for an ODE parameter estimation problem, please refer to the tutorial for the <a href="../Beer/#Beer_tut">Beer model</a>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Beer/">« Models with many conditions specific parameters</a><a class="docs-footer-nextpage" href="../Parameter_estimation/">Parameter estimation »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 14 August 2023 20:30">Monday 14 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/Best_options/index.html

@@ -13,4 +13,4 @@
                                      odeSolverOptions=ODESolverOptions(CVODE_BDF(), abstol=1e-8, reltol=1e-8), 
                                      odeSolverGradientOptions=ODESolverOptions(CVODE_BDF(), abstol=1e-8, reltol=1e-8),
                                      gradientMethod=:Adjoint, 
-                                     sensealg=InterpolatingAdjoint()) </code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Gradient_hessian_support/">« Supported gradient and hessian methods</a><a class="docs-footer-nextpage" href="../API_choosen/">API »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 14 August 2023 17:52">Monday 14 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+                                     sensealg=InterpolatingAdjoint()) </code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Gradient_hessian_support/">« Supported gradient and hessian methods</a><a class="docs-footer-nextpage" href="../API_choosen/">API »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 14 August 2023 20:30">Monday 14 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/Boehm/index.html

@@ -31,4 +31,4 @@
 @printf("First element in the gradient = %.2e\n", gradient[1])
 @printf(&quot;First element in the hessian = %.2f\n&quot;, hessian[1, 1])</code></pre><pre><code class="nohighlight hljs">Cost = 138.22
 First element in the gradient = 2.20e-02
-First element in the hessian = 2199.49</code></pre><h2 id="Where-to-go-from-here"><a class="docs-heading-anchor" href="#Where-to-go-from-here">Where to go from here</a><a id="Where-to-go-from-here-1"></a><a class="docs-heading-anchor-permalink" href="#Where-to-go-from-here" title="Permalink"></a></h2><p>Next, we suggest you take a look at the <a href="../Best_options/#best_options">Choosing best options for a PEtab problem</a> guide. Additionally, we recommend exploring the <a href="../Gradient_hessian_support/#gradient_support">Supported gradient and hessian methods</a> section. In case you want to provide your model-file as a Julia-file instead of an SBML file take a look at <a href="../Beer_julia_import/#Beer_Julia_import">Providing a model as a Julia file instead of an SBML File</a>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../Brannmark/">Models with pre-equilibration (steady-state simulation) »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 14 August 2023 17:52">Monday 14 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+First element in the hessian = 2199.49</code></pre><h2 id="Where-to-go-from-here"><a class="docs-heading-anchor" href="#Where-to-go-from-here">Where to go from here</a><a id="Where-to-go-from-here-1"></a><a class="docs-heading-anchor-permalink" href="#Where-to-go-from-here" title="Permalink"></a></h2><p>Next, we suggest you take a look at the <a href="../Best_options/#best_options">Choosing best options for a PEtab problem</a> guide. Additionally, we recommend exploring the <a href="../Gradient_hessian_support/#gradient_support">Supported gradient and hessian methods</a> section. In case you want to provide your model-file as a Julia-file instead of an SBML file take a look at <a href="../Beer_julia_import/#Beer_Julia_import">Providing a model as a Julia file instead of an SBML File</a>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../Brannmark/">Models with pre-equilibration (steady-state simulation) »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 14 August 2023 20:30">Monday 14 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>