FAQ

I can't import libsbml, libsedml, or libcombine in Tellurium.

• These packages are available under the names tesbml, tesedml, and tecombine so as not to conflict with the official packages.

After installing Tellurium notebook a second time, I get a message saying "The Tellurium Python kernel failed to start. It may be missing or non-functional. Your Tellurium installation may be corrupt"

• Please wipe out or move your app data directory:
  • On Windows, it is C:\Users\<username>\AppData\Roaming\Tellurium (or something similar).
  • On Mac, it is ~/Library/Application Support/Tellurium (please note the space, which needs to be escaped if using the shell)
  • On Linux, it is ~/.config/Tellurium

On Mac, after downloading Tellurium, I can't open it because it is from an unidentified developer.

• Apple requires all developers to pay $100/year for an account. This poses a problem for academic free/open-source software, which is typically maintained on a pro bono basis. You can bypass this message as follows:
  • Open the Terminal app from the /Applications/Utilities/ folder and then enter the following command:
    • sudo spctl --master-disable
  • Hit return and authenticate with an admin password

Does the Tellurium installation make any changes to my Python installation?

• The Notebook and IDE frontends are designed to not interfere with any pre-existing Python installations. They each install a private Python environment on your storage drive. The pip packages install into your Python site-packages directory, like all pip packages.

Does Tellurium support constraint-based modeling?

• Tellurium does not have built-in support for constraint-based modeling per se. However, cobrapy is a Python package which does support constraint-based modeling. It can be installed in Tellurium by running the following Python code:

import tellurium as te
te.installPackage('cobra')

After installing cobra, you can import it like so:

import cobra

The windows version of Tellurium comes bundled with cobrapy already.

Can notebooks saved with the Tellurium notebook viewer be used with Jupyter?

• The Tellurium notebook viewer supports special features such as inline OMEX cells. These notebooks cannot be read by Jupyter. The Tellurium notebook viewer can export notebooks to a Jupyter-compatible format.

Are the Tellurium packages signed?

• PyPI packages and Linux notebook releases are signed with Kyle Medley's GPG key: 9BE0E97B

Which SBML packages are supported?

• Due to an issue in libSEDML, we currently build libSBML with legacy math. This precludes the Arrays, Multi, and Spatial packages. All other packages are available.

I have a problem with the Tellurium notebook viewer not covered here. What should I do?

• You can find more troubleshooting information for the notebook viewer here.

I am a Mac user and I want Tellurium Spyder but it's not supported anymore!

• Currently, we only provide legacy support for Tellurium Spyder on Mac OS X. From Tellurium version 1.3.5 and onwards, no new binaries will be built and distributed. However, you can still configure your Python distribution to enjoy similar experience. First, we suggest you install Python 2.7 or 3.6 version of anaconda. Next, simply run pip install tellurium or <path to anaconda installation>/bin/pip install tellurium if the terminal complains about not being able to find pip. Now run Spyder that comes with anaconda and use tellurium to model, analyze, and simulate!

A number of the simulation examples in the textbook "Systems Biology: Introduction to Pathway Modeling" no longer appears to work? What can I do?

• There have been a number of API changes since the book's publication and this is what is causing the model scripts to fail. At present there are two options to fix this: 1) Install an older version of Tellurium that is compatible, eg 1.2 (https://sourceforge.net/projects/pytellurium/files/Tellurium-1.2/). 2) Wait for a new edition of the book in 2018, this will be compatible with the latest Tellurium edition.