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segrelab / comets-toolbox

MATLAB scripts and utilities for the COMETS software for spatial DFBA
http://www.bu.edu/segrelab/comets/
GNU Lesser General Public License v3.0
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Environmental Variable #7

Closed sshort325 closed 2 years ago

sshort325 commented 2 years ago

Screen Shot 2022-06-28 at 10 23 22 AM I keep getting this issue and I'm not sure how to fix it.

dukovski commented 2 years ago

so you need to have only one line with GUROBI_COMETS_HOME in the file

sshort325 commented 2 years ago

Comment? Oh okay, I think I have a few so I just want the new one

dukovski commented 2 years ago

Yup

sshort325 commented 2 years ago

Screen Shot 2022-06-28 at 12 55 14 PM Got it that time

dukovski commented 2 years ago

Great, does cometspy work now?

sshort325 commented 2 years ago

Im not sure this is what I get when I do the first part of "Loading the COMETS Python Toolbox" Screen Shot 2022-06-28 at 4 39 00 PM

dukovski commented 2 years ago

This is a problem with cobra now. You need to install it properly. Do it on anaconda shell $ pip install cobra

sshort325 commented 2 years ago

Where do I find the anaconda shell?

sshort325 commented 2 years ago

Screen Shot 2022-06-28 at 6 57 03 PM

dukovski commented 2 years ago

You can actually do it in a regular terminal.

dukovski commented 2 years ago

Follow the instructions in cobrapy. https://opencobra.github.io/cobrapy/

sshort325 commented 2 years ago

Screen Shot 2022-06-29 at 11 01 24 AM This is what I get after following the pip install cobra

sshort325 commented 2 years ago

Screen Shot 2022-06-29 at 11 00 44 AM And i get the same in my python

dukovski commented 2 years ago

Hm, not sure. Look at this discussion: https://groups.google.com/g/cobra-pie/c/G4b1bFwmkSk

sshort325 commented 2 years ago

I found out it's because "Cobra.test" has been deprecated for the newer "load_model", so it is fixed for me now. Thank you so much for all your help! I really appreciate it!

dukovski commented 2 years ago

Great, so comets is running now?

sshort325 commented 2 years ago

I did the "import cometspy as c" and it works just fine. It just let me know that I haven't used it yet.

dukovski commented 2 years ago

Great, have fun with it. Can you tell me who you are, what university and what you will be using it for? Thx.

sshort325 commented 2 years ago

Yes. My name is Samantha Short, for Carroll College in Montana. Maize Microbiome Modeling Project: Predict bacterial metabolic and growth responses (individually and in the community) to different nutrient sources, which I thought would be really interesting to explore with COMETS and to see how spatiotemporal dynamics plays a role.

dukovski commented 2 years ago

That's fantastic. Please contact me if you need any additional help with comets. I will close this issue now, if that's fine with you.

sshort325 commented 2 years ago

Yes, thank you again for all your help! I will reach out if I have any other issues.