Creating multiple perturbations

[kthobe]

Hi Aurelien,
I want to use your tool to test a lot of perturbations (mostly more than one at a time) on my model. One perturbation worked fine for me, but double doesn't, it just gives me the unperturbed attractors. So when I say "A%1" that works, but "A%1,B%1" even A and B are not restricted.
I noticed that your example in the colomoto notebook "bioLQM_tutorial.ipynb" does the same thing, when you set "CycD%1" it only gives you the cyclic attractor with CycD=1, but if you do the combination "CycD%1,Rb%1" you get your original unperturbed attractors.

What does work is redefining the model twice:
pert = biolqm.perturbation(model, "A%1")
pert2 = biolqm.perturbation(pert, "B%1")

But that would be much more complicated, when trying to automate testing for > 100 perturbations with varying numbers of alterations.

Cheers, Kirsten

[aurelien-naldi]

Hi Kirsten,
it's a typo in the example notebook: it should work if you separate the multiple perturbations with a space instead of a comma

I will fix the notebook and make it work with both.

[kthobe]

Great, thanks for the quick response that works. Bwt, the documentation ( http://www.colomoto.org/biolqm/doc/modifier-perturbation.html) is also not clear about this, it says: *List of perturbations*Define multiple individual perturbations, with a comma-separated list of the above elements. For example A%0,B%1 defines the double knockout of A and B. The first sentence is clear, but the second also has the typo. Thanks again! Am Mi., 24. Feb. 2021 um 18:14 Uhr schrieb Aurélien Naldi < notifications@github.com>:

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Hi Kirsten, it's a typo in the example notebook: it should work if you separate the multiple perturbations with a space instead of a comma I will fix the notebook and make it work with both. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#23 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AETJWLZKFKA7SJCGLPEW6ULTAUXXHANCNFSM4YE4IQQA> .

[pauleve]

@aurelien-naldi any hope to fix the notebook for the next release on the 1st?

[aurelien-naldi]

Thanks for the ping! I fixed the notebook, but the change in the code will wait until the next release (which will enable documentation support in bioLQM).