Add binder links and landing page (#1937)

* move .binder/ to binder/, as jupyter lab won't allow us accessing hidden directories by default
* add landing page for easier access of different notebooks [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/AMICI-dev/AMICI/binder_landing?labpath=binder%2Foverview.ipynb)
* binder link to readme / doc

README.md

@@ -85,7 +85,8 @@ To install AMICI, first read the installation instructions for
 [Matlab](https://amici.readthedocs.io/en/develop/matlab_installation.html).
 
 To get you started with Python-AMICI, the best way might be checking out this
-[Jupyter notebook](https://github.com/AMICI-dev/AMICI/blob/master/documentation/GettingStarted.ipynb).
+[Jupyter notebook](https://github.com/AMICI-dev/AMICI/blob/master/documentation/GettingStarted.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/AMICI-dev/AMICI/develop?labpath=documentation%2FGettingStarted.ipynb).
 
 To get started with Matlab-AMICI, various examples are available
 in [matlab/examples/](https://github.com/AMICI-dev/AMICI/tree/master/matlab/examples).

.binder/README.md → binder/README.md

@@ -1,4 +1,4 @@
-# .binder/
+# binder/repo2docker configuration
 
 Configuration files for [binder](https://mybinder.org/) / repo2docker.
 

binder/overview.ipynb

@@ -0,0 +1,43 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "f7ebed12-4309-4c92-a54e-da80ccd2d5e7",
+   "metadata": {},
+   "source": [
+    "# AMICI example notebooks\n",
+    "\n",
+    "* [Getting started](../documentation/GettingStarted.ipynb)\n",
+    "\n",
+    "  Brief intro to AMICI for first-time users.\n",
+    "\n",
+    "* [Example \"steadystate\"](../python/examples/example_steadystate/ExampleSteadystate.ipynb)\n",
+    "\n",
+    "  A more detailed introduction to the AMICI interface, demonstrating sensitivity analysis, various options, finite difference checks, ...\n",
+    "\n",
+    "* [PEtab import / simulation](../python/examples/example_petab/petab.ipynb)\n",
+    "\n",
+    "  How to import and simulate PEtab problems.\n",
+    "\n",
+    "* [Experimental conditions](../python/examples/example_presimulation/ExampleExperimentalConditions.ipynb)\n",
+    "\n",
+    "  How to represent different experimental conditions in AMICI and how to use preequilibration.\n",
+    "  \n",
+    "* [Steadystate (sensitivities)](../python/examples/example_constant_species/ExampleEquilibrationLogic.ipynb)\n",
+    "\n",
+    "  Describes and demonstrates the various algorithms for computing steady states and steady-state sensitivities."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "",
+   "name": ""
+  },
+  "language_info": {
+   "name": ""
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

documentation/python_interface.rst

@@ -137,6 +137,9 @@ We also plan to implement support for the
 Examples
 ========
 
+.. image:: https://mybinder.org/badge_logo.svg
+ :target: https://mybinder.org/v2/gh/AMICI-dev/AMICI/develop?labpath=binder%2Foverview.ipynb
+
 .. toctree::
    :maxdepth: 1