Copyright 2014-2023 Kiri Choi, J Kyle Medley, Matthias König, Kaylene Stocking, Caroline Cannistra, Michal Galdzicki, Ciaran Welsh, Lucian Smith, Adel Heydarabadipour, and Herbert Sauro
Tellurium is a python environment for reproducible dynamical modeling of biological networks. Tellurium provides the interfacial code to convert between standard formats and utilize powerful libraries without requiring technical expertise, allowing you to focus on what’s important: building better models. Tellurium also provides first-class support for exchangeability via COMBINE archives, allowing you to share your models and simulations with other tools.
Tellurium combines state-of-the-art scientific Python libraries, such as NumPy and SciPy, and includes special-purpose systems biology Python tools. Out of the box, Tellurium includes libroadrunner, antimony, phrasedml, libsbml, and libsedml.
The Tellurium (and libroadrunner project) project is funded from the NIH/NIGMS (GM081070) and NIH/NIBIB U24EB028887.
import tellurium as te
rr = te.loada('''
model example0
S1 -> S2; k1*S1
S1 = 10
S2 = 0
k1 = 0.1
end
''')
result = rr.simulate(0, 40, 500)
te.plotArray(result)
:exclamation:Attention to those using Python 2.7 : Python 2.7 reached EOL on January 1st, 2020. Support for Python 2.7 has been dropped, though previous releases will continue to be available.
Tellurium can be installed as a Python package, with a front-end (Notebook, IDE), or in a cloud environment (Google Colab):
A. Python package (pip)
B. IDE front-end based on Spyder
C. Notebook front-end
D. Google Colab
We recommend first-time users choose one of the front-ends, while developers looking to integrate Tellurium use the pip package. All python desktop IDE graphical front-ends should work. We know for certain that telluirum will work from Spyder, pyCharm and Visual Studio Code.
The IDE front-end provides a MATLAB like experience with a code editor and Python console. The notebook front-end provides a notebook interface similar to Jupyter, and features notebook cells for inline OMEX, a human-readable representation of COMBINE archives.
For any issues with installation and setup, please check FAQ or contact us.
If you have a version of Python in an environment you're comfortable with, you can add Tellurium with pip:
pip install tellurium
Tellurium itself is Python-only, and is available for any version of Python 3. Its main binary dependency, roadrunner, should be installed with Tellurium, and should be available for the latest three or four versions of Python (currently 3.8, 3.9, 3.10, and 3.11), for Windows, Mac (both Intel and ARM), and Linux.
For those using Anaconda, we currently do not have a separate Anaconda version of Tellurium, so you'll need to install it via pip, as above.
:exclamation:For detailed instructions on how to setup Tellurium on Anaconda distributions, see this page.
For developers, the latest stable version from the repository can be installed via
pip install git+https://github.com/sys-bio/tellurium.git
The Tellurium Spyder installers are tested with Windows 10 and 11, and come with a choice of Python versions.
:exclamation:Attention to those upgrading to Tellurium Spyder IDE from an older version : We strongly suggest you to completely remove the older version of Tellurium Spyder IDE prior to installing the latest version.
If you wish to use a different version of Python, you'll need to install Tellurium from the windows command line by using the command: pip install tellurium
NOTE: Installation requires administrative rights. It is recommended to accept the default settings.
Tellurium can be used with Thonny, a free, open-source IDE for Python that is designed for beginners.
*.exe
to start the installationtellurium
in the search box and press the "Search on PyPI" buttontellurium
package is found in "Search results", click on it, and then press the "Install" button. Wait until the installation process is completed.The Tellurium notebook is no longer being updated, but is still available. It was tested with Windows 10. The notebook viewer comes with Python 3.6 (64-bit).
*.exe
to start the installation
For Mac users there a a number of options. By far, the easiest is to use the self-cotbained Thonny Python IDE.
Tellurium can be used with Thonny, a free, open-source IDE for Python that is designed for beginners.
*.pkg
to start the installationtellurium
in the search box and press the "Search on PyPI" buttontellurium
package is found in "Search results", click on it, and then press the "Install" button. Wait until the installation process is completed.Follow the installer instructions.. The installer will install Spyder as part of the installation process. If you customize the installation, you will have a chance to select which packages to install - ensure Spyder is selected.
When prompted, add Anaconda to your PATH (optional, but this will make the following steps easier).
Open a Terminal and run the command:
conda install msgpack-python
Next, install Tellurium itself:
pip install tellurium
If this fails, try using the default absolute path to Anaconda, which will probably be something like:
/Users/<your-user>/opt/anaconda3/bin/pip install tellurium
Launch the Anaconda Navigator via Launchpad. In Anaconda Navigator, run Spyder and then try import tellurium
within the Spyder editor or console.
Currently, only a Legacy version of the Mac Spyder IDE is available. We recommend using the Notebook front-end on Mac.
The Tellurium notebook is no longer being updated, but is still available. It was tested with Mac OS X 10.10+. The notebook viewer comes with Python 3.6 (64-bit).
*.dmg
file to open a new windowFor those who wish to use Tellurium with Spyder IDE on Mac OS X, we also suggest that you install through Anaconda by following the instructions on this page.