========
Appendix
========

Source Code Repositories
========================

Tellurium is a collection of Python packages developed inside and outside our group, including simulators, libraries for reading and writing standards like SBML and SED-ML, and various utilities (e.g. `sbml2matlab <https://github.com/stanleygu/sbml2matlab>`_). Tellurium itself is a Python module that provides integration between these various subpackages and its source code is `hosted on GitHub <https://github.com/sys-bio/tellurium>`_. A list of constituent packages and repositories is given below:

* `tellurium <https://github.com/sys-bio/tellurium>`_: This project.
* `libroadrunner <https://github.com/sys-bio/roadrunner>`_: SBML ODE / stochastic simulator.
* `antimony <https://github.com/sys-bio/antimony>`_: A human-readable representation of SBML.
* `phrasedml <https://github.com/sys-bio/phrasedml>`_: A human-readable representation of SED-ML.
* `libcombine <https://github.com/sbmlteam/libCombine>`_: A library for reading/writing COMBINE archives.
* `sbml2matlab <https://github.com/sys-bio/sbml2matlab>`_: A utility for converting SBML models to MATLAB ODE simulations.
* `simplesbml <http://sys-bio.github.io/simplesbml/>`_: A utility for creating SBML models without the complexity of libSBML.
* `libsbml <https://sourceforge.net/projects/sbml>`_: A library for reading/writing `SBML <http://sbml.org/Main_Page>`_.
* `libsedml <https://github.com/fbergmann/libSEDML>`_: A library for reading/writing SED-ML.

License
=======

The `Tellurium source code <https://github.com/sys-bio/tellurium>`_ is licensed under the Apache License 2.0. Tellurium uses third-party dependencies which may be licensed under different terms. Consult the documentation for the respective third-party packages for more details.

Contact
=======

* For questions about Tellurium, please visit our `tellurium-discuss Google group <https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!forum/tellurium-discuss>`_.

* For new feature requests or to report bugs, see `Tellurium on GitHub. <https://github.com/sys-bio/tellurium/issues/>`_ and create an issue.

Funding
=======

The Tellurium project is funded by generous support from **NIH/NIGMS** grant GM081070. The content is solely the responsibility of the authors and does not necessarily represent the views of the National Institutes of Health.

Acknowledgments
===============

Tellurium relies on many great open-source projects, including the `Spyder IDE <https://www.spyder-ide.org/>`_, `nteract <https://github.com/nteract/nteract>`_, `Python <https://www.python.org/>`_, `numpy <http://www.numpy.org/>`_, `Jupyter <http://jupyter.org/>`_, CVODE, NLEQ, AUTO2000, `LAPACK <http://www.netlib.org/lapack/>`_, `LLVM <https://llvm.org/>`_, and `the POCO libraries <https://pocoproject.org/>`_. Tellurium also relies on open source contributions from Frank Bergmann (libStruct, `libSEDML <https://github.com/fbergmann/libSEDML>`_), Mike Hucka,  Sarah Keating (`libSBML <https://sourceforge.net/projects/sbml>`_), and Pierre Raybaut.