Need help with CobraPy installation! (New to python and cobrapy)

[Yiming Yang]

Hello,

Could anyone provide me a step-to-step instruction on how to install CobraPy? 

I've installed python and downloaded a folder called "cobra-0.23.0.tar.gz" from https://pypi.org/project/cobra/#files, but I have no idea how to install it.

I tried double-clicking on the setup.py file in that folder, but nothing happened : (

I would be grateful if anyone could help me with this.

Thanks in advance

[Dennis van den Berg]

Dear Yiming Yang,

Check the first link in https://cobrapy.readthedocs.io/en/latest/ 

You do not need to download cobrapy. Just use pip or conda (depending on how you installed python) but install.rst explains it all.

Good luck,

Dennis

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[Yiming Yang]

Thank you Dennis,

I'll take a look at the instructions :D

Regards,

Yiming

[Stephen Chapman]

pip install worked great for me!

[valeria ansaldo saavedra]

after installing cobra py with pip, how can i install and use escher with the cobrapy? please

[bs22]

Here are the step by step codes to install cobrapy and other useful packages:

1. python3 -m venv cobrapy (create environment)
2. source cobrapy/bin/activate (activate environment)
3. python -m pip install cobra (install cobrapy)
4. python -m pip install escher (install escher)
5. python -m pip install plotly (install plotly)
6. python -m pip install matplotlib (install matplot)
7. python -m pip install -e git+https://github.com/biosustain/cameo.git@devel#egg=cameo (install cameo)

Cheers!

BS

[valeria ansaldo saavedra]

Thank you very much! Can you help me with something else? I opened a model in Cobrapy, in Json format. Im able to see the model but what i want to do is to add new reactions to simulate a new metabolic route that uses alginate as carbon source for the production of a biofuel metabolite. What do you reccomend or could you help me? Thanks in advance

Valeria

[Dennis van den Berg]

Hi Valeria,

Did you check https://cobrapy.readthedocs.io/en/latest/ yet? In chapter two the addition of new metabolites and reactions are explained.

There is also a readthedocs.io for Escher.

Tip: For the naming of metabolites and selecting the correct formulas: Search the database used by your original model for any new metabolites and reactions you want to add.

Good luck with your modelling,

Dennis

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[valeria ansaldo saavedra]

Thank you so much Dennis,

Yes I checked the documentation but it is sometimes a bit complicated for me to understand. So in chapter two, the same instructions work for existing models for example, I downloaded a Json model from Bigg and opened in cobrapy, i just do the same as described in chapter two? But how do I use the Model.get_by_id in this case? 

Thank you so much for your help again,

Valeria