Marko Vendelin markov
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  • Joined on 2022-10-24
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markov opened issue hamed/Bayesian-fcs#45 2024-02-19 21:22:36 +02:00
Allow to save limited number of trajectories
markov opened issue hamed/Bayesian-fcs#44 2024-02-19 08:39:48 +02:00
Implement motion from the closest location in PyMC
markov pushed to main at divya/energy_transfer 2024-02-07 18:10:07 +02:00
900c539179 Fixing some bugs
markov pushed to main at hamed/Bayesian-fcs 2024-02-07 10:38:32 +02:00
67aa8ec43c Sync priors for numpyro and pymc
522fea9d14 Make priors for multiple particles different
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markov pushed to main at hamed/Bayesian-fcs 2024-02-07 08:30:42 +02:00
de979d3b48 Drop PyQt6 from requirements
markov created branch steady-state in divya/energy_transfer 2024-02-06 18:06:58 +02:00
markov pushed to steady-state at divya/energy_transfer 2024-02-06 18:06:58 +02:00
88c419d716 Add steady state checks
markov pushed to main at mari/5-state-XB-model 2024-01-29 20:22:58 +02:00
a7b0c66e5d Add gitignore
7f32313a8c Add missing ODE solver
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markov commented on issue divya/energy_transfer#1 2023-12-15 10:18:22 +02:00
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vo2 = v*0.2 why is that?

when referring to experimental data, please specify paper and figure / subplot.

exp_data = exp_data * 806 - this is not good. instead, make a var with CS…

markov commented on issue divya/energy_transfer#1 2023-12-15 10:11:49 +02:00
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usually, we use micromol / min / g prot. please use this unit for rates and then convert to nmol O2 when needed for comparison.

already have question regarding PK_vmax - not sure regarding the…

markov commented on issue divya/energy_transfer#1 2023-12-15 09:49:12 +02:00
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Each constant has to have a reference next to it. If it is based on my recommendation then state that in the code too.

mg prot should always be spelled out. Right now it is hard to read comment…

markov commented on issue divya/energy_transfer#1 2023-12-06 14:46:05 +02:00
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class PK:
    def __init__(self, vmax, Kib=0.4, Kia=1e+4):
        self.vmax = vmax
        self.KiaKb = Kia*Kib ; self.Kib = Kib ; self.Kia = Kia
    
    def rate(self, ADP, PEP):
   …
markov commented on issue divya/energy_transfer#1 2023-12-05 11:55:32 +02:00
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  • PK reaction: make it then as random bi reaction between PEP and ADP. Just set PEP dissociation constant to a small one, so it would have a minimal impact on the rate. Then handle PEP as a almost…
markov opened issue divya/energy_transfer#1 2023-11-28 14:36:34 +02:00
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