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sys-bio / tellurium

Python Environment for Modeling and Simulating Biological Systems
http://tellurium.analogmachine.org/
Apache License 2.0
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Tellurium 2.0.0 feedback/issues #196

Closed matthiaskoenig closed 7 years ago

matthiaskoenig commented 7 years ago

Hi all, here some feedback to the tellurium 2.0.0 interface. Just tried it on Ubuntu 16.04 and here some feedback

typo

example notebooks missing/confusing

I expected to find some example notebooks, i.e. the notebooks from the publication packaged with the app. When clicking on

Where are the example notebooks of the publication? Create an introductory notebook which shows/documents:

There are lots of tellurium example notebooks which should be included.

After opening tellurium for the first time one sits there and does not really know what to do now. Perhaps an introductory text cell at the top of a new notebook giving the basic information like

Save SBML model not working

When creating a model in a model cell via:

model test
    J0: S1 -> S2; k1*S1;
    S1 = 10.0; S2 = 0.0;
    k1 = 0.1
end
Success: Model can be accessed via variable test

And than trying to save via the save icon in the model cell, the menu for saving pops up and after giving a filename I get Save SBML /home/mkoenig/Desktop/test1.xml but no file is saved on the harddisk.

Omex archives not loading

I tried loading some omex archives, but just get a generic error that omex could not be loaded: Some examples are available here, which should be loaded https://github.com/SED-ML/sed-ml/tree/master/specification/level-1-version-3/examples Like for instance the following: https://github.com/SED-ML/sed-ml/blob/master/specification/level-1-version-3/examples/2d-parameter-scan/2d-parameter-scan.omex?raw=true

The error is very generic, it would help to get a detailled error message to know what is the problem, i.e. provide the stack traces if imports are not working of OMEX, SBML and CELL-ML files.

No phrasedml cell & SED-ML import

There is no option/icon for import SED-ML, also there is no phrased-ml cell type. What is the reason for this?

Some additional things:

M edit: I am updating this when I find new things. Feel free to separate in individual issues.

0u812 commented 7 years ago

Many thanks for your feedback, Matthias. New binaries are available at the download page. Update on all issues: