Update readme

README.md

@@ -5,23 +5,24 @@
 [![GitHub issues](https://img.shields.io/github/issues/jcrozum/biobalm?style=flat-square)](https://github.com/jcrozum/biobalm/issues) 
 [![License](https://img.shields.io/pypi/l/biobalm?style=flat-square)](https://github.com/jcrozum/biobalm/blob/main/LICENSE)
 
-# Boolean Attractor Landscape Mapper (biobalm)
+# Boolean Attractor Landscape Mapper (`biobalm`)
 
-biobalm is a Python library for exploring the attractor landscape of large-scale Boolean networks with hundreds or thousands of variables. It combines symbolic (BDD) and automated (ASP) reasoning to efficiently construct a *succession diagram* of a Boolean network: an inclusion-based acyclic graph of the network's trap spaces. biobalm can then use this succession diagram to accelerate attractor search and infer control strategies for target trap spaces.
+`biobalm` is a Python library for exploring the attractor landscape of large-scale Boolean networks with hundreds or thousands of variables. It combines symbolic (BDD) and automated (ASP) reasoning to efficiently construct a *succession diagram* of a Boolean network: an inclusion-based acyclic graph of the network's trap spaces. biobalm can then use this succession diagram to accelerate attractor search and infer control strategies for target trap spaces.
+
+ > `biobalm` is accompanied by an analysis artefact that benchmarks it against `pystablemotifs`, `mts-nfvs` and `aeon.py`. The artefact also compares the succession diagrams generated by published biological Boolean networks to random network ensembles and finds significant differences in structure. The artefact is available at [Zenodo](https://doi.org/10.5281/zenodo.13854760) and [Github](https://github.com/jcrozum/balm-analysis).
 
 ### Installation
 
-biobalm is on PyPI: **TODO: PyPI release coming soon. Use git method (below).**
+`biobalm` is on PyPI:
 
 ```
 pip install biobalm
 ```
 
-The base installation allows you to generate succession diagrams and control strategies, plus some easier-to-find attractors. However, to enable the full attractor detection functionality, you need to also install `pint` and `mole`:
+The base installation should enable all core functionalities (generate succession diagrams and control strategies, find attractor seeds states and attractor sets). Optionally, you can also use `pint` during attractor identification as a static analysis step:
 
  - Native binaries of `pint` can be obtained [here](https://loicpauleve.name/pint/doc/#Binaries).
- - Download `mole` [here](http://www.lsv.fr/~schwoon/tools/mole/), compile it (simply run `make`), and make sure the result is in your `$PATH`.
-
+
 You can also install the latest version of biobalm directly from github:
 
 ```
@@ -30,11 +31,23 @@ pip install git+https://github.com/jcrozum/biobalm.git@main
 
 ### Referencing biobalm
 
-**TODO: A publication describing biobalm in detail will be available soon. Until then, please link this github repository instead.**
+`biobalm` is on [bioRxiv](https://www.biorxiv.org/content/10.1101/2024.09.30.615897v1):
 
-### Using biobalm
+```
+@article {biobalm,
+	author = {Trinh, Van-Giang and Park, Kyu Hyong and Pastva, Samuel and Rozum, Jordan C},
+	title = {Mapping the attractor landscape of Boolean networks},
+	elocation-id = {2024.09.30.615897},
+	year = {2024},
+	doi = {10.1101/2024.09.30.615897},
+	publisher = {Cold Spring Harbor Laboratory},
+	URL = {https://www.biorxiv.org/content/early/2024/10/02/2024.09.30.615897},
+	eprint = {https://www.biorxiv.org/content/early/2024/10/02/2024.09.30.615897.full.pdf},
+	journal = {bioRxiv}
+}
+```
 
-To learn more about how biobalm functions, you can explore the example notebooks listed below. Alternatively, biobalm's API documentation is also available [online](https://jcrozum.github.io/biobalm/).
+### Using biobalm
 
-**TODO: Usage examples coming soon.**
+To learn more about how biobalm functions, API documentation is available [online](https://jcrozum.github.io/biobalm/). You can also explore the analysis artefact mentioned above for more in-depth examples of biobalm usage.