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

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.