README and documentation updates

README.md

@@ -26,7 +26,27 @@ pip install thunor
 
 ## Examples and documentation
 
-See [Thunor Core documentation](https://core.thunor.net).
+The Thunor Core documentation is available [online](https://core.thunor.net),
+or you can build it locally for offline use. To do so, clone this git
+repository and change into the `thunor` directory.
+
+To build documentation locally, you'll need a few software dependencies:
+
+    pip install -r doc/requirements.txt
+
+Then, you can build the documentation like so:
+
+    cd doc
+    make html
+
+After the build completes, open _build/html/index.html in your web browser.
+
+## Tutorial
+
+To manually work through the tutorial from the documentation above, you can
+open the file with Jupyter Notebook:
+
+    jupyter notebook --NotebookApp.iopub_data_rate_limit=1.0e10 doc/tutorial.ipynb
 
 ## Further help and resources
 

doc/tutorial.ipynb

@@ -12,20 +12,42 @@
    "metadata": {},
    "source": [
     "**Thunor** (pronounced THOO-nor) is a free software platform for managing,\n",
-    "visualizing, and analyzing high throughput screen (HTS) data, which measure\n",
-    "the dose-dependent response of cells to one or more drug(s).\n",
+    "visualizing, and analyzing high throughput cell proliferation data,\n",
+    "which measure the dose-dependent response of cells to one or more drug(s).\n",
     "\n",
-    "This repository, Thunor Core, is a Python package which can be used for\n",
-    "standalone analysis or integration into computational pipelines.\n",
+    "This repository, [Thunor Core](https://github.com/alubbock/thunor), is a\n",
+    "Python package which can be used for standalone analysis or integration\n",
+    "into computational pipelines.\n",
     "\n",
-    "A web interface is also available, called Thunor Web."
+    "A web interface is also available, called [Thunor Web](https://github.com/alubbock/thunorweb).\n",
+    "Thunor Web has a [comprehensive manual](https://docs.thunor.net), which goes\n",
+    "into further detail about the curve fitting methods, types of plots\n",
+    "available and other information you may find relevant.\n",
+    "\n",
+    "Please see the [Thunor website](https://www.thunor.net) for additional resources,\n",
+    "and a link to our chat room, where you can ask questions about Thunor."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## A note about online documentation\n",
+    "\n",
+    "This documentation is available [online](https://core.thunor.net) or by\n",
+    "building it locally. Unforunately, there is [a known issue](https://github.com/rtfd/sphinx_rtd_theme/pull/545)\n",
+    "that sometimes prevents some of the plots below from displaying online. We're\n",
+    "awaiting a fix from our documentation host, readthedocs. In the meantime,\n",
+    "please try refreshing the page, or you can [build the documentation locally as described in the README](https://github.com/alubbock/thunor). The latter approach is recommended,\n",
+    "since as it gives you a chance to edit and extend this Jupyter Notebook\n",
+    "to explore how Thunor Core works."
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## [Ignore] Set up code for documentation"
+    "### [Ignore] Set up code for online documentation"
    ]
   },
   {
@@ -64,7 +86,8 @@
     "\n",
     "    jupyter notebook --NotebookApp.iopub_data_rate_limit=1.0e10\n",
     "    \n",
-    "The data rate limit needs to be increased or `init_notebook_mode()` throws an error."
+    "The data rate limit needs to be increased or `init_notebook_mode()` throws an error.\n",
+    "This is a [plotly requirement](https://community.plot.ly/t/tips-for-using-plotly-with-jupyter-notebook-5-0-the-latest-version/4156)."
    ]
   },
   {
@@ -78,7 +101,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "First, specify a file to load. This can be done as a string filename, but here we load an example dataset from the thunor package."
+    "First, specify a file to load. This can be done as a string filename, but here we load an example dataset from the thunor package itself, but you can also another filename."
    ]
   },
   {