diff --git a/README.md b/README.md index 52856ae214..f9f1aea0d2 100644 --- a/README.md +++ b/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). diff --git a/.binder/README.md b/binder/README.md similarity index 80% rename from .binder/README.md rename to binder/README.md index 3ff2958774..4739de23aa 100644 --- a/.binder/README.md +++ b/binder/README.md @@ -1,4 +1,4 @@ -# .binder/ +# binder/repo2docker configuration Configuration files for [binder](https://mybinder.org/) / repo2docker. diff --git a/.binder/apt.txt b/binder/apt.txt similarity index 100% rename from .binder/apt.txt rename to binder/apt.txt diff --git a/binder/overview.ipynb b/binder/overview.ipynb new file mode 100644 index 0000000000..22c17a4ef8 --- /dev/null +++ b/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 +} diff --git a/.binder/postBuild b/binder/postBuild similarity index 100% rename from .binder/postBuild rename to binder/postBuild diff --git a/.binder/runtime.txt b/binder/runtime.txt similarity index 100% rename from .binder/runtime.txt rename to binder/runtime.txt diff --git a/.binder/start b/binder/start similarity index 100% rename from .binder/start rename to binder/start diff --git a/documentation/python_interface.rst b/documentation/python_interface.rst index dc57f8a200..920d278a3c 100644 --- a/documentation/python_interface.rst +++ b/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