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genssi-developer / GenSSI

GenSSI 2.0 - Generating Series for testing Structural Identifiability
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Thyroid1 and Thyroid2 identical #6

Closed JanHasenauer closed 7 years ago

JanHasenauer commented 7 years ago

I did not find a difference between Thyroid1 and Thyroid2. What is the difference?

thomassligon commented 7 years ago

These are COMBOS models, and the difference in the COMBOS versions of Thyroid1 and Thyroid2 is the initial conditions. This difference has somehow been lost in the GenSSI version. I will correct that.

Tom (Dr. Thomas S. Ligon) Tom@thomassligon.infomailto:Tom@thomassligon.info Frohnloher Str. 6a 81475 Muenchen Germany Tel. +49(89)74575075

From: JanHasenauer [mailto:notifications@github.com] Sent: Monday, September 11, 2017 11:40 PM To: genssi-developer/GenSSI GenSSI@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [genssi-developer/GenSSI] Thyroid1 and Thyroid2 identical (#6)

I did not find a difference between Thyroid1 and Thyroid2. What is the difference?

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genssi-developer commented 7 years ago

In COMBOS, Thyroid1 has no initial conditions, and Thyroid2 has all zeros. In GenSSI we have model.sym.x0=[0 0 0] for both models. Question: Is it possible to define empty initial conditions in AMICI/GenSSI? I tried setting model.sym.x0=[] and the result is not good, i.e. no Lie derivatives, no tableaus. Should we add a check in genssiCheckModel?

JanHasenauer commented 7 years ago

I think that GenSSI needs conceptually initial conditions. We should however get the same results if we set the initial conditions in GenSSI to unknown parameters and perform the structural identifiability analysis only with respect to the kinetic parameters.

genssi-developer commented 7 years ago

I see that Thyroid1 now has three new parameters, x10, x20, and x30, but they are not used, and x0 is still all zeros.

genssi-developer commented 7 years ago

Closed unintentionally.

JanHasenauer commented 7 years ago

ah, good point. i included them in x0. now it should be fine.