Conserved quantities (e.g adp + atp)

biosustain / Maud

Enzyme models that take into account kinetics, allostery and thermodynamics

https://maud-metabolic-models.readthedocs.io/en/latest/

GNU General Public License v3.0

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Conserved quantities (e.g adp + atp) #190

Open teddygroves opened 4 years ago

NicholasCowie commented 1 year ago

Ideally precalculate and let the user know that there are conserved moieties. This will ensure that the user will have to define the pool rather than the ODE solver determining it. Maud should then select the state variables which are independent and then calculate the other within stan as an algebraic set of equations

carrascomj commented 11 months ago

New parameter for pool sizes in python, passed to Stan.
Function for the left nullspace in python.
Pass the left nullspace to stan.
Change ode_bdf_tol to dae.
Set new constraint $Lx = a$ where $a$ is the pool sizes, $L$ is the left nullspace and $x$ is the concentration (balanced).