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

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teddygroves opened this issue Nov 14, 2019 · 2 comments
Open

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

teddygroves opened this issue Nov 14, 2019 · 2 comments
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@teddygroves
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@teddygroves teddygroves added the NEXT Next on the list to do label Sep 20, 2023
@NicholasCowie
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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
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carrascomj commented Nov 20, 2023 •
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  • 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).

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@teddygroves @NicholasCowie @carrascomj