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Kiri Choi edited this page Aug 6, 2018 · 48 revisions

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.

Mac OS X Gatekeeper Screenshot

  • 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

How do I uninstall Tellurium notebook?

  • On Mac, simply drag the Tellurium icon from your Applications folder to the trash.
  • On Windows, go to Control Panel, then Add / Remove Programs, then select Tellurium and click "Uninstall."
  • On Linux, use the package manager to remove the package: sudo dnf remove Tellurium (Red Hat) or sudo apt-get remove Tellurium (Debian).
  • In all cases this will still leave Tellurium's Python installation on your system, which must be manually removed.
    • On Mac, delete the directory ~/Library/Application Support/Tellurium
    • On Windows, delete the directory C:\Users\<username>\AppData\Roaming\Tellurium (the directory may be different if you have a non-standard system configuration)
    • On Linux, delete the directory ~/.config/Tellurium

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?

I would like to use Tellurium on Anaconda. What should I do?

  • Installing Tellurium on Anaconda is quite simple. First, install Anaconda for Windows, Mac OS X, or Linux. Installation instructions are available for Windows, Mac OS X, and Linux. If you are using Mac OS X or Linux, make sure to enter yes to Do you wish the installer to prepend the Anaconda install location to PATH? if asked.

  • Once Anaconda is installed, open Anaconda Prompt (Windows) or a Terminal window (Mac OS X, Linux) and run the following command:

pip install tellurium

which will install tellurium as a package.

  • Anaconda comes with Spyder IDE. To run it, open Anaconda Navigator and launch Spyder IDE. To know more about Anaconda Navigator, refer to Getting started with Navigator and Anaconda Navigator. You may also launch Spyder IDE by running spyder command in Anaconda Prompt or a Terminal window. If you are having issue running Spyder IDE, check this section.

  • That's it! Now you should be able to use Tellurium and assorted packages on Anaconda.

I tried to use Tellurium on Anaconda, but Spyder IDE crashes with Segmentation fault (core dumped)!

  • Try installing pyopengl on Anaconda by running following command:
conda install pyopengl

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?

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 appear 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.
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