docs

Author: younik

docs/index.rst

@@ -9,15 +9,14 @@ ChromaX: a fast and scalable breeding program simulator
 ChromaX is a Python library that enables the simulation of genetic recombination, genomic estimated
 breeding value calculations, and selection processes.
 The library is based on `JAX <https://jax.readthedocs.io>`_ to exploit parallelization.
-It can smoothly operate on CPU, GPU (NVIDIA, AMD, and Intel), or TPU.
-
-.. note::
-
-  At the moment, JAX, thus ChromaX supports Apple silicon GPU exclusively through the Metal plug-in, which is still in the experimental release phase.
-  For additional information, please refer to `Apple's JAX on Metal documentation <https://developer.apple.com/metal/jax/>`_.
+It can smoothly operate on CPU, GPU (NVIDIA, Apple, AMD, and Intel), or TPU.
 
 Installation
 ===================================
+.. note::
+
+  To exploit parallelization capabilities of your hardware, it is recommended to install jax manually. 
+  You can find the instruction for your hardware in `google/jax <https://github.com/google/jax?tab=readme-ov-file#installation>`_.
 
 You can install the library via Python Package manager `pip`:
 
@@ -38,19 +37,20 @@ To cite ChromaX in publications:
 
 .. code-block:: bibtex
 
-  @article{Younis2023.05.29.542709,
-    abstract = {ChromaX is a Python library that enables the simulation of genetic recombination, genomic estimated breeding value calculations, and selection processes. By utilizing GPU processing, it can perform these simulations up to two orders of magnitude faster than existing tools with standard hardware. This offers breeders and scientists new opportunities to simulate genetic gain and optimize breeding schemes.},
-    author = {Omar G. Younis and Matteo Turchetta and Daniel Ariza Suarez and Steven Yates and Bruno Studer and Ioannis N. Athanasiadis and Andreas Krause and Joachim M. Buhmann and Luca Corinzia},
-    doi = {10.1101/2023.05.29.542709},
-    elocation-id = {2023.05.29.542709},
-    eprint = {https://www.biorxiv.org/content/early/2023/05/31/2023.05.29.542709.1.full.pdf},
-    journal = {bioRxiv},
-    publisher = {Cold Spring Harbor Laboratory},
-    title = {ChromaX: a fast and scalable breeding program simulator},
-    url = {https://www.biorxiv.org/content/early/2023/05/31/2023.05.29.542709.1},
-    year = {2023},
-    bdsk-url-1 = {https://www.biorxiv.org/content/early/2023/05/31/2023.05.29.542709.1},
-    bdsk-url-2 = {https://doi.org/10.1101/2023.05.29.542709}
+  @article{10.1093/bioinformatics/btad691,
+      author = {Younis, Omar G and Turchetta, Matteo and Ariza Suarez, Daniel and Yates, Steven and Studer, Bruno and Athanasiadis, Ioannis N and Krause, Andreas and Buhmann, Joachim M and Corinzia, Luca},
+      title = "{ChromaX: a fast and scalable breeding program simulator}",
+      journal = {Bioinformatics},
+      volume = {39},
+      number = {12},
+      pages = {btad691},
+      year = {2023},
+      month = {11},
+      abstract = "{ChromaX is a Python library that enables the simulation of genetic recombination, genomic estimated breeding value calculations, and selection processes. By utilizing GPU processing, it can perform these simulations up to two orders of magnitude faster than existing tools with standard hardware. This offers breeders and scientists new opportunities to simulate genetic gain and optimize breeding schemes.The documentation is available at https://chromax.readthedocs.io. The code is available at https://github.com/kora-labs/chromax.}",
+      issn = {1367-4811},
+      doi = {10.1093/bioinformatics/btad691},
+      url = {https://doi.org/10.1093/bioinformatics/btad691},
+      eprint = {https://academic.oup.com/bioinformatics/article-pdf/39/12/btad691/54143193/btad691.pdf},
   }
 
 .. toctree::