From 36b2121edc899118ad016746f6ca53a9c2a059af Mon Sep 17 00:00:00 2001 From: blakeaw Date: Fri, 24 Feb 2023 10:52:54 -0600 Subject: [PATCH] Switched the extracellular volume back to 10x the cell volume to be consistent with current simulations. --- CHANGELOG.md | 1 - parm/compartments.py | 4 ++-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 02e1efc..d017a93 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,6 @@ * `util.run_model` has an input parameter `nprocs` that is passed to the solver's `run` function as `num_processors` to allow for parallel execution of the inputs if multiple parameter sets or initial conditions are provided. * Moved `parm.variants.classic` to `parm.variants.twostate.classic`. * Moved the existing `parm.variants.precoupled` to `parm.variants.twostate.precoupled`. -* `parm.receptor_modules` updated the extracellular volume to be 1000x the cell volume like the BNGL examples. ### Added * `util.load_pydream_chains` function that can load the sampled parameter vectors output from PyDREAM sampling chains. diff --git a/parm/compartments.py b/parm/compartments.py index 5023640..7327e90 100644 --- a/parm/compartments.py +++ b/parm/compartments.py @@ -157,7 +157,7 @@ def default_cell(): # https://github.com/RuleWorld/BNGTutorial/blob/master/CBNGL/LRR_comp.bngl # https://github.com/RuleWorld/BNGTutorial/blob/master/CBNGL/LR_comp.bngl # We'll use 10 time the cytosolic volume - Parameter("Vextra", Vcyto.value * 1000) + Parameter("Vextra", Vcyto.value * 10) # Volume of the ER lumen/cisternal space. # It is often >10% of cell volume according to # Alberts et al. https://www.ncbi.nlm.nih.gov/books/NBK26841/ . @@ -265,7 +265,7 @@ def hek293_cell(): # https://github.com/RuleWorld/BNGTutorial/blob/master/CBNGL/LRR_comp.bngl # https://github.com/RuleWorld/BNGTutorial/blob/master/CBNGL/LR_comp.bngl # We'll use 10 time the cytosolic volume - Parameter("Vextra", Vcyto.value * 1000) + Parameter("Vextra", Vcyto.value * 10) # Volume of the ER lumen/cisternal space. # It is often >10% of cell volume according to # Alberts et al. https://www.ncbi.nlm.nih.gov/books/NBK26841/ .