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combine-org / combine-notebooks

COMBINE python notebooks showcasing the libraries
https://co.mbine.org/examples
GNU Lesser General Public License v3.0
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Add SBOL repressilator example #5

Open matthiaskoenig opened 2 years ago

matthiaskoenig commented 2 years ago

Gonzalo Vidal presented a repressilator SBOL notebook during HARMONY2022. Latest version is available at http://t.ly/loica. It contains some example code on how to create the repressilator in SBOL based on parts.

aditya-ml commented 2 years ago

Can you re-share the link? It seems to have expired.

Gonza10V commented 2 years ago

Hi here is the Colab notebook: https://drive.google.com/file/d/1xxxMS5amaTGY2Z09i5h03zMr2J2zGiwg/view?usp=sharing

Here is another notebook that you can use and that also has the repressilator example: https://github.com/RudgeLab/LOICA/blob/master/notebooks/LOICA_DEMO_Operators.ipynb

Look for 'SBOL connection' in both. I can add the example if you want, tell me where and the pattern that I should follow.

Let me know if can help you with something else 😉

aditya-ml commented 2 years ago

Hi @Gonza10V I've referred through your ipynb notebook for adding a repressilator example, but I'm running into ModuleNotFoundErrors.

Could you check this script and create a working SBOL example in example_sbol.py file here: https://github.com/combine-org/combine-notebooks/tree/libsbml-notebook/src/combine_notebooks ?