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<li class="toctree-l1"><a class="reference internal" href="tutorial01.html">1. Brief Tour of E-Cell4 Simulations</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorial01.html#1.1.-Quick-Demo">1.1. Quick Demo</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial01.html#1.2.-Spatial-Simulation-and-Visualization">1.2. Spatial Simulation and Visualization</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial02.html">2. How to Build a Model</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorial02.html#2.1.-Species">2.1. Species</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial04.html">4. How to Run a Simulation</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="tutorial04.html#4.3.-Capsulizing-Algorithm-into-a-Factory-Class">4.3. Capsulizing Algorithm into a Factory Class</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial05.html">5. How to Log and Visualize Simulations</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorial05.html#5.1.-Logging-Simulations-with-Observers">5.1. Logging Simulations with Observers</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial06.html">6. How to Solve ODEs with Rate Law Functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorial06.html#6.1.-ReactionRuleDescriptor">6.1. ReactionRuleDescriptor</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial06.html#6.2.-ReactionRuleDescriptorPyFunc">6.2. ReactionRuleDescriptorPyFunc</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial07.html">7. Introduction of Rule-based Modeling</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorial07.html#7.1.-count_species_matches">7.1. count_species_matches</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial07.html#7.2.-ReactionRule.count-and-generate">7.2. ReactionRule.count and generate</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial07.html#7.3.-NetfreeModel">7.3. NetfreeModel</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial07.html#7.4.-Differences-between-Species,-ReactionRule-and-NetfreeModel">7.4. Differences between Species, ReactionRule and NetfreeModel</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial08.html">8. More about 1. Brief Tour of E-Cell4 Simulations</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorial08.html#8.1.-Creating-ODEWorld">8.1. Creating ODEWorld</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial08.html#8.2.-How-to-Use-Real3">8.2. How to Use Real3</a></li>
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<li class="toctree-l2"><a class="reference internal" href="tutorial08.html#8.4.-Switching-the-Solver">8.4. Switching the Solver</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial09.html">9. Spatial Gillespie Method</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorial09.html#9.1.-Spaces-in-E-Cell4">9.1. Spaces in E-Cell4</a></li>
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<li class="toctree-l2"><a class="reference internal" href="tutorial09.html#9.3.-Defining-Molecular-Diffusion-Coefficient">9.3. Defining Molecular Diffusion Coefficient</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial09.html#9.4.-Molecular-localization">9.4. Molecular localization</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial09.html#9.5.-Molecular-initial-location-and-the-reaction">9.5. Molecular initial location and the reaction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial10.html">10. Spatiocyte Simulations at Single-Molecule Resolution</a><ul>
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