Add more usage examples on doc
@@ -12,6 +12,8 @@ To run the examples, clone the git repository:
and use the `Tellurium notebook viewer <http://tellurium.readthedocs.io/en/latest/installation.html#front-end-1-tellurium-notebook>`_ or `Jupyter <http://jupyter.readthedocs.org/en/latest/install.html>`_ to open any notebook in the ``tellurium/examples/notebooks/core`` directory.
+Tellurium Spyder comes with these examples under Tellurium Spyder installation directory. Look for folder called ``tellurium-winpython-examples``.
+
--------------------
Basics
--------------------
@@ -22,7 +24,7 @@ Basics
Models & Model Building
-------------------------
-In this section model the creation of example models is shown.
+In this section, various types of models and different ways to building models are shown.
.. include:: _notebooks/core/model_modelFromBioModels.rst
.. include:: _notebooks/core/model_nonUnitStoichiometries.rst
@@ -31,6 +33,19 @@ In this section model the creation of example models is shown.
.. include:: _notebooks/core/model_generatingDifferentWaveforms.rst
.. include:: _notebooks/core/model_normalizedSpecies.rst
+-------------------------------
+Simulation and Analysis Methods
+-------------------------------
+
+In this section, different ways to simlate and analyse a model is shown.
+
+.. include:: _notebooks/core/computeSteadyState.rst
+.. include:: _notebooks/core/tellurium_stochastic.rst
+.. include:: _notebooks/core/parameter_scan.rst
+.. include:: _notebooks/core/plot2DParameterScan.rst
+.. include:: _notebooks/core/steadystate_scan.rst
+.. include:: _notebooks/core/tellurium_reset.rst
+
--------
SED-ML
--------
@@ -72,3 +87,13 @@ examples which correspond to common motifs in biological networks (negative feed
To draw the network diagrams seen here, you will need `graphviz <http://www.graphviz.org/>`_ installed.
.. include:: _notebooks/core/tellurium_examples.rst
+
+-------------
+Miscellaneous
+-------------
+
+If you are using Tellurium notebook or Tellurium Spyder, you can install additional package using ``installPackage`` function. In Tellurium Spyder, you can also install packages using included command Prompt. For more information, see `Running Command Prompt for Tellurium Spyder <https://tellurium.readthedocs.io/en/latest/walkthrough.html#running-command-prompt-for-tellurium-spyder>`_.
+
+.. autofunction:: tellurium.installPackage
+
+.. include:: _notebooks/core/methods_installing_packages.rst
