Unable to run cameo design --product vanillin

[mauriceling]

Hi, I am trying to run through the guide but I get this response:

(py36) C:>cameo design --product vanillin Error: no such option: --product

(py36) C:>

[fma91]

You should try to run it in ipython. Load a model an then:

predictor = pathway_prediction.PathwayPredictor(model) pathways = predictor.run(product="vanillin", max_predictions="select the number of predictons" )

Or try this other way also in ipython:

from cameo.api import design design(product='compound')

[phantomas1234]

@mauriceling sorry about that, there is indeed no --product option (you can check with cameo design --help). So the command should be cameo design vanillin. I'll fix the docs. But I'd also recommend to go with @fma91 suggestions as it will allow you to better post-process the results. We never really got around making the output of the command line interface produce useful outputs. Also, as a shameless advertisement, you could give our new cell factory design platform a try https://caffeine.dd-decaf.eu (the platform contains also many more useful features, like interactive pathway simulations and visualizations etc.) and let us know what you think.

[mauriceling]

Hi Nikolaus

Thank you for your advice. At the moment, I am trying to interface Cameo with our tool, AdvanceSyn Toolkit (github.com/mauriceling/advancesyntoolkit). However, I do face a a few other issues.

Will it be possible to get in touch with you directly for assistance?

Thanks Maurice

On Fri, 22 Mar 2019, 5:13 PM Nikolaus Sonnenschein, < [email protected]> wrote:

@mauriceling https://github.com/mauriceling sorry about that, there is indeed no --product option (you can check with cameo design --help). So the command should be cameo design vanillin. I'll fix the docs. But I'd also recommend to go with @fma91 https://github.com/fma91 suggestions as it will allow you to better post-process the results. We never really got around making the output of the command line interface produce useful outputs. Also, as a shameless advertisement, you could give our new cell factory design platform a try https://caffeine.dd-decaf.eu (the platform contains also many more useful features, like interactive pathway simulations and visualizations etc.) and let us know what you think.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/biosustain/cameo/issues/236#issuecomment-475545823, or mute the thread https://github.com/notifications/unsubscribe-auth/AB4naHCpQMs85cky9kKMvm2gY9d9Kwq7ks5vZJ6agaJpZM4cCuiZ .

[phantomas1234]

@mauriceling please keep the issues coming if you have any. For more direct assistance you can chat with us on https://gitter.im/biosustain/cameo. Not to discourage you or anything, but your modeling language looks pretty close to what http://tellurium.analogmachine.org already provides?

[mauriceling]

Sure, I'll keep the issues coming.

Thank you for your thumbs-up on tellurium. There is indeed substantial similarity. You can even say that we are inspired by tellurium but currently, I've only implemented the core - more features up soon.

On Fri, 22 Mar 2019, 5:31 PM Nikolaus Sonnenschein, < [email protected]> wrote:

@mauriceling https://github.com/mauriceling please keep the issues coming if you have any. For more direct assistance you can chat with us on https://gitter.im/biosustain/cameo. Not to discourage you or anything, but your modeling language looks pretty close to what http://tellurium.analogmachine.org already provides?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/biosustain/cameo/issues/236#issuecomment-475551222, or mute the thread https://github.com/notifications/unsubscribe-auth/AB4naM1UFmP_qC65U2mUO09yLl7f3QQaks5vZKLbgaJpZM4cCuiZ .