.. simble documentation master file, created by
   sphinx-quickstart on Tue Sep 30 10:47:34 2025.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

.. raw:: html

   <div class="admonition-announcement attention">
      <p class="admonition-title">In review</p>
      This software is currently under review and the API may change before its final release.
      <br><br>
   </div>

Welcome to SimBLE!
====================

.. raw:: html

   <p>
   <img src="_static/simble_logo.png" alt="SimBLE logo" 
   style="float:left; width:84px; height:84px; margin-right: 10px;margin-bottom:10px;"><span style="vertical-align:top">SimBLE is a BCR evolution simulator. It starts with a naive heavy and light chain pair, and models evolution and selection in the germinal center as well as migration out of germinal center. SimBLE also has customizable sampling.</span>
   </p>


.. include:: how_simble_works.rst

.. include:: contact.rst

.. include:: authors.rst


Getting Started
----------------
We recommend starting with the :ref:`quickstart`. 

If you are interested in contributing to SimBLE, please see :ref:`development`.


.. toctree::
   :maxdepth: 2
   :caption: Contents:

   quickstart
   examples
   development
   modules


.. include:: citing.rst

.. include:: license.rst

.. toctree::
   :maxdepth: 2
   :caption: Related Resources:
   :hidden:

   all_arguments
   how_simble_works
   glossary

------------------

:ref:`SimBLE Glossary<glossary>`

:ref:`Site Index<genindex>`

:ref:`Module Index<modindex>`