README: add examples, pipx (#185)

* README: add examples, pipx

* pypi badge

* Update README.md

Co-authored-by: Paul Jonas Jost <70631928+PaulJonasJost@users.noreply.github.com>

---------

Co-authored-by: Paul Jonas Jost <70631928+PaulJonasJost@users.noreply.github.com>

Author: dweindl

README.md

@@ -1,6 +1,7 @@
+[![PyPI - Version](https://badge.fury.io/py/PEtab-GUI.svg)](pypi.org/project/PEtab-GUI/)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15355753.svg)](https://doi.org/10.5281/zenodo.15355753)
-# PEtabGUI
 
+# PEtabGUI
 
 PEtabGUI provides a graphical user interface to inspect and edit parameter
 estimation problems encoded in the
@@ -16,6 +17,13 @@ To install PEtabGUI from [PyPI](https://pypi.org/project/PEtab-GUI/), run:
 pip install petab_gui
 ```
 
+or, to install PEtabGUI in a dedicated virtual environment using
+[pipx](https://github.com/pypa/pipx) (to be installed separately), run:
+
+```bash
+pipx install petab_gui
+```
+
 ### From GitHub
 
 To install the latest development version from GitHub, run:
@@ -46,6 +54,17 @@ After installation, launch PEtabGUI from the command line using the
 Optionally, you can provide the path to an existing PEtab YAML file
 as an argument.
 
+### Examples
+
+A set of real-world PEtab problems is available in the
+[PEtab benchmark collection](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab).
+
+Download and unpack the [archive](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/archive/refs/heads/master.zip),
+then open one of the YAML files inside `Benchmark-Models/*/` using
+PEtabGUI.
+`Benchmark-Models/Boehm_JProteomeRes2014/Boehm_JProteomeRes2014.yaml`
+should serve as a good starting point.
+
 ## Features
 
 The PEtabGUI provides a Python-based graphical user interface that simplifies