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Nov 20, 2024
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L1v5 #81

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eea2229
Update to l1v5.
luciansmith Nov 18, 2024
2aa0645
Updated compiled files for website [skip ci]
Nov 18, 2024
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Binary file added documents/sed-ml-L1V5.pdf
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30 changes: 15 additions & 15 deletions examples.html
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Expand Up @@ -172,7 +172,7 @@ <h2>L1V3 examples (in COMBINE archives)</h2>
<div>
Verified simulation tool(s):
<ul class="comma-separated-list">
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.8</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.10</li>
</ul>
</div>

Expand Down Expand Up @@ -212,8 +212,8 @@ <h2>L1V3 examples (in COMBINE archives)</h2>
<div>
Verified simulation tool(s):
<ul class="comma-separated-list">
<li><a href="https://biosimulators.org/simulators/pysces">PySceS</a> 1.0.0</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.8</li>
<li><a href="https://biosimulators.org/simulators/pysces">PySCeS</a> 1.2.2</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.10</li>
</ul>
</div>

Expand Down Expand Up @@ -283,7 +283,7 @@ <h2>L1V3 examples (in COMBINE archives)</h2>
<div>
Verified simulation tool(s):
<ul class="comma-separated-list">
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.8</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.10</li>
</ul>
</div>

Expand Down Expand Up @@ -313,7 +313,7 @@ <h2>L1V3 examples (in COMBINE archives)</h2>
<div>
Verified simulation tool(s):
<ul class="comma-separated-list">
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.8</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.10</li>
</ul>
</div>

Expand Down Expand Up @@ -344,7 +344,7 @@ <h2>L1V3 examples (in COMBINE archives)</h2>
<div>
Verified simulation tool(s):
<ul class="comma-separated-list">
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.8</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.10</li>
</ul>
</div>

Expand Down Expand Up @@ -375,7 +375,7 @@ <h2>L1V3 examples (in COMBINE archives)</h2>
<div>
Verified simulation tool(s):
<ul class="comma-separated-list">
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.8</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.10</li>
</ul>
</div>

Expand Down Expand Up @@ -406,7 +406,7 @@ <h2>L1V3 examples (in COMBINE archives)</h2>
<div>
Verified simulation tool(s):
<ul class="comma-separated-list">
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.8</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.10</li>
</ul>
</div>

Expand Down Expand Up @@ -443,7 +443,7 @@ <h2>L1V3 examples (in COMBINE archives)</h2>
Verified simulation tool(s):
<ul class="comma-separated-list">
<li><a href="https://biosimulators.org/simulators/gillespy2">GillesPy2</a> 1.6.6</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.8</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.10</li>
</ul>
</div>

Expand Down Expand Up @@ -474,7 +474,7 @@ <h2>L1V3 examples (in COMBINE archives)</h2>
<div>
Verified simulation tool(s):
<ul class="comma-separated-list">
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.8</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.10</li>
</ul>
</div>

Expand Down Expand Up @@ -520,7 +520,7 @@ <h2>L1V3 examples (in COMBINE archives)</h2>
<div>
Verified simulation tool(s):
<ul class="comma-separated-list">
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.8</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.10</li>
</ul>
</div>

Expand Down Expand Up @@ -550,8 +550,8 @@ <h2>L1V3 examples (in COMBINE archives)</h2>
<div>
Verified simulation tool(s):
<ul class="comma-separated-list">
<li><a href="https://biosimulators.org/simulators/pysces">PySceS</a> 1.0.0</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.8</li>
<li><a href="https://biosimulators.org/simulators/pysces">PySCeS</a> 1.2.2</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.10</li>
</ul>
</div>

Expand Down Expand Up @@ -611,8 +611,8 @@ <h2>L1V3 examples (in COMBINE archives)</h2>
<div>
Verified simulation tool(s):
<ul class="comma-separated-list">
<li><a href="https://biosimulators.org/simulators/pysces">PySceS</a> 1.0.0</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.8</li>
<li><a href="https://biosimulators.org/simulators/pysces">PySCeS</a> 1.2.2</li>
<li><a href="https://biosimulators.org/simulators/tellurium">tellurium</a> 2.2.10</li>
</ul>
</div>

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10 changes: 4 additions & 6 deletions index.html
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Expand Up @@ -141,15 +141,13 @@ <h1 class="page-header"><i class="fa fa-fw fa-home"></i> What is SED-ML?</h1>
reproducibility of simulation experiments.
</p>
<p>
The current version is <a href="documents/sed-ml-L1V4.pdf" target="_blank"><b>SED-ML Level 1 Version
4</b></a>.
For additional specification documents and proposals see the <a href="specifications.html" title="Specifications">Specifications</a>
page.
The current version is <a href="documents/sed-ml-L1V5.pdf" target="_blank"><b>SED-ML Level 1 Version 5</b></a>.
For additional specification documents and proposals see the <a href="specifications.html" title="Specifications">Specifications</a> page.
</p>
<a href="documents/sed-ml-L1V4.pdf" target="_blank">
<a href="documents/sed-ml-L1V5.pdf" target="_blank">
<span class="btn btn-default" style="font-weight: bold;">
<img alt="logo" src="images/logoSEDML_w90_t.png"/>
L1V4 (official specification document)
L1V5 (official specification document)
<img alt="pdf" src="images/pdf.png"/>
</span>
</a>
Expand Down
2 changes: 2 additions & 0 deletions showcase.html
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Expand Up @@ -373,6 +373,7 @@ <h2>SED-ML libraries</h2>
<li>L1V2</li>
<li>L1V3</li>
<li>L1V4</li>
<li>L1V5</li>
</ul>
</td>
<td>C++ library for reading and writing SED-ML. Swig languange bindings for C#, Java, Python, R and Ruby.</td>
Expand Down Expand Up @@ -486,6 +487,7 @@ <h2>SED-ML tools</h2>
<li>L1V2</li>
<li>L1V3</li>
<li>L1V4</li>
<li>L1V5</li>
</ul>
</td>
<td>Software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie`s stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. COPASI supports impor and export of SED-ML files.</td>
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1 change: 1 addition & 0 deletions site_creator/templates/db/libraries.yaml
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Expand Up @@ -46,6 +46,7 @@ libraries:
- L1V2
- L1V3
- L1V4
- L1V5

- name: 'libSedML (old version)'
link: 'http://libsedml.sf.net'
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1 change: 1 addition & 0 deletions site_creator/templates/db/tools.yaml
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Expand Up @@ -91,6 +91,7 @@ tools:
- L1V2
- L1V3
- L1V4
- L1V5
modelLanguages:
- SBML

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10 changes: 4 additions & 6 deletions site_creator/templates/index.html
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Expand Up @@ -14,15 +14,13 @@ <h1 class="page-header"><i class="fa fa-fw fa-home"></i> What is SED-ML?</h1>
reproducibility of simulation experiments.
</p>
<p>
The current version is <a href="documents/sed-ml-L1V4.pdf" target="_blank"><b>SED-ML Level 1 Version
4</b></a>.
For additional specification documents and proposals see the <a href="specifications.html" title="Specifications">Specifications</a>
page.
The current version is <a href="documents/sed-ml-L1V5.pdf" target="_blank"><b>SED-ML Level 1 Version 5</b></a>.
For additional specification documents and proposals see the <a href="specifications.html" title="Specifications">Specifications</a> page.
</p>
<a href="documents/sed-ml-L1V4.pdf" target="_blank">
<a href="documents/sed-ml-L1V5.pdf" target="_blank">
<span class="btn btn-default" style="font-weight: bold;">
<img alt="logo" src="images/logoSEDML_w90_t.png"/>
L1V4 (official specification document)
L1V5 (official specification document)
<img alt="pdf" src="images/pdf.png"/>
</span>
</a>
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20 changes: 14 additions & 6 deletions site_creator/templates/specifications.html
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Expand Up @@ -16,10 +16,10 @@ <h1 class="page-header"><i class="fa fa-fw fa-file-code-o"></i> SED-ML Specifica
<tr>
<td><b>Latest release:</b></td>
<td>
<a href="documents/sed-ml-L1V4.pdf" target="_blank">
<a href="documents/sed-ml-L1V5.pdf" target="_blank">
<span class="btn btn-success" style="font-weight: bold;">
<img alt="logo" src="images/logoSEDML_w90_t.png" height="25"/>
L1V4
L1V5
<img alt="pdf" src="images/pdf.png" height="35"/>
</span>
</a>
Expand All @@ -33,10 +33,10 @@ <h1 class="page-header"><i class="fa fa-fw fa-file-code-o"></i> SED-ML Specifica
</td>
<!--
<td>
<a href="https://github.com/SED-ML/sed-ml/raw/master/specification/level-1-version-4/sed-ml-L1V4.pdf" target="_blank">
<a href="https://github.com/SED-ML/sed-ml/raw/master/specification/level-1-version-4/sed-ml-L1V5.pdf" target="_blank">
<span class="btn btn-warning" style="font-weight: bold;">
<img alt="logo" src="images/logoSEDML_w90_t.png" height="25"/>
L1V4 draft
L1V5 draft
<img alt="pdf" src="images/pdf.png" height="35"/>
</span>
</a>
Expand Down Expand Up @@ -124,14 +124,22 @@ <h3>Proposals</h3>

<h2>All specifications</h2>
<p>
<a href="documents/sed-ml-L1V4.pdf" target="_blank">
<a href="documents/sed-ml-L1V5.pdf" target="_blank">
<span class="btn btn-default" style="font-weight: bold;">
L1V4 (official specification document)
L1V5 (official specification document)
<img alt="pdf" src="images/pdf.png" height="35"/>
</span>
</a>
</p>
<p>
<a href="documents/sed-ml-L1V4.pdf" target="_blank">
<span class="btn btn-default" style="font-weight: bold;">
L1V4 (official specification document)
<img alt="pdf" src="images/pdf.png" height="35"/>
</span>
</a>
</p>
<p>
<a href="documents/sed-ml-L1V3.pdf" target="_blank">
<span class="btn btn-default" style="font-weight: bold;">
L1V3 (official specification document)
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20 changes: 14 additions & 6 deletions specifications.html
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Expand Up @@ -143,10 +143,10 @@ <h1 class="page-header"><i class="fa fa-fw fa-file-code-o"></i> SED-ML Specifica
<tr>
<td><b>Latest release:</b></td>
<td>
<a href="documents/sed-ml-L1V4.pdf" target="_blank">
<a href="documents/sed-ml-L1V5.pdf" target="_blank">
<span class="btn btn-success" style="font-weight: bold;">
<img alt="logo" src="images/logoSEDML_w90_t.png" height="25"/>
L1V4
L1V5
<img alt="pdf" src="images/pdf.png" height="35"/>
</span>
</a>
Expand All @@ -160,10 +160,10 @@ <h1 class="page-header"><i class="fa fa-fw fa-file-code-o"></i> SED-ML Specifica
</td>
<!--
<td>
<a href="https://github.com/SED-ML/sed-ml/raw/master/specification/level-1-version-4/sed-ml-L1V4.pdf" target="_blank">
<a href="https://github.com/SED-ML/sed-ml/raw/master/specification/level-1-version-4/sed-ml-L1V5.pdf" target="_blank">
<span class="btn btn-warning" style="font-weight: bold;">
<img alt="logo" src="images/logoSEDML_w90_t.png" height="25"/>
L1V4 draft
L1V5 draft
<img alt="pdf" src="images/pdf.png" height="35"/>
</span>
</a>
Expand Down Expand Up @@ -251,14 +251,22 @@ <h3>Proposals</h3>

<h2>All specifications</h2>
<p>
<a href="documents/sed-ml-L1V4.pdf" target="_blank">
<a href="documents/sed-ml-L1V5.pdf" target="_blank">
<span class="btn btn-default" style="font-weight: bold;">
L1V4 (official specification document)
L1V5 (official specification document)
<img alt="pdf" src="images/pdf.png" height="35"/>
</span>
</a>
</p>
<p>
<a href="documents/sed-ml-L1V4.pdf" target="_blank">
<span class="btn btn-default" style="font-weight: bold;">
L1V4 (official specification document)
<img alt="pdf" src="images/pdf.png" height="35"/>
</span>
</a>
</p>
<p>
<a href="documents/sed-ml-L1V3.pdf" target="_blank">
<span class="btn btn-default" style="font-weight: bold;">
L1V3 (official specification document)
Expand Down