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Curveball: Predicting competition results from growth curves
============================================================

**Author**: `Yoav Ram <http://www.yoavram.com>`_

Curveball is an open-source software for analysis and  
visualization of high-throughput growth curve data 
and prediction of competition experiment results.

Curveball:

* fits **growth models** to **growth curve data** to estimate values of **growth traits**
* uses estimated **growth traits** and **competition models** to predict results of **competition experiments**
* infers **fitness** and **selection coefficients** from predicted **competition results**


Who is this for?
----------------

Curveball is for researchers who want to analyze growth curve data using 
a framework that integrates **population dynamics** and **population genetics**,
allowing the inference and interpretation of **differences in fitness** 
between strains in terms of **differences in growth traits**.

Curveball provides a **command line interface** (CLI) and an **programmatic interface** (API) 
that can directly work with collections of growth curve measurements (e.g., 96-well plates).

**No programmings skills** are required for using the CLI; 
basic familiarity with the **Python programming language** is recommended for using the API.

.. note::
   
   This documentation provides technical details on using Curveball.
   For more information on the theoretical and computational aspects of Curveball, read the paper:

   .. pull-quote::

      Ram, Dellus-Gur, Bibi, Karkare, Obolski, Feldman, Cooper, Berman, Hadany. (2019) `Predicting microbial relative growth in a mixed culture from growth curve data <https://doi.org/10.1073/pnas.1902217116>`_. *Proceedings of the National Academy of Science USA*. doi:10.1073/pnas.1902217116

   or the preprint:

   .. pull-quote::

      Ram et al. (2015) `Predicting competition results from growth curves <https://dx.doi.org/10.1101/022640>`_. *bioRxiv*. doi:10.1101/022640.


Quickstart
----------

Install `Anaconda with Python 3 <https://www.anaconda.com/downloads>`_, then run:

>>> python -m pip install curveball
>>> curveball --help

For more detailed instructions, Proceed to the :doc:`Installation instructions <install>` and then to the :doc:`tutorial`.


Contents
--------

.. toctree::
   :maxdepth: 1

   install
   tutorial
   ioutils
   plots
   models
   baranyi_roberts_model
   likelihood
   competitions
   cli
   troubleshooting

API
---

* :ref:`genindex`
* :ref:`modindex`

References
----------

* `Documentation <https://curveball.yoavram.com>`_
* Source code: `GitHub  <https://github.com/yoavram/curveball>`_
* Download: `PyPI <https://pypi.org/project/curveball/>`_
* Bugs, comments or questions: `GitHub Issues <https://github.com/yoavram/curveball/issues>`_
* Buildbot: `Travis-CI <https://magnum.travis-ci.com/yoavram/curveball>`_
* Code coverage: `Codecov <http://codecov.io/github/yoavram/curveball>`_
* `Change log <https://github.com/yoavram/curveball/tree/master/CHANGELOG.md>`_
* `Contributing <https://github.com/yoavram/curveball/blob/master/CONTRIBUTING.md>`_

.. note::
   
   Curveball source code and examples are licensed under the terms of the `MIT license <http://opensource.org/licenses/MIT>`_.
   
   Curveball documentation, examples, and other materials are licensed under the terms of the `Creative Commons Attribution 4.0 International (CC BY 4.0) license <https://creativecommons.org/licenses/by/4.0/>`_.

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