mcsim two dimen gif
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This dialog is used to setup and run a two dimensional Monte Carlo simulation with sampling of parameter distributions in the outer loop and for each set of samples record either an

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New MCSim now simulates SBML models Example left of SBML model yeast glycolysis renderred by JDesigner and GNU MCSim simulated time course of the model s chemical species right

mcsim three dim evpi gif
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This dialog is used to setup and run a three dimensional Monte Carlo simulation with sampling of parameter distributions for partial EVPI calculation in the outermost loop the remaining

Yeast OD png
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and a Table and a plot like these ones are preferable You can see that at the early steps only time points from the low dose experiment are included except time zero and the last time You can trace on the Figure which points are included

J0 Ki 3 chains png
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The three chains have merged and mix well but it is always useful to check visually the convergence by forming such plots Figure 4 Trajectories of 3 Markov chains for the first 3 parameter sampled at convergence over the last half million runs The 3 trajectories overlap on each panel and are

Yeast 10000pts w data png
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data To generate a synthetic dataset Gaussian error 10 CV was added to points along each species trajectories at 7 times including time zero Here is what the data used look like Figure 3 Plot of the simulated data dots used for the Bayesian calibration Three files 1

J0 Kglc 3 chains png
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a summary of the marginal parameters posterior distributions The three chains have merged and mix well but it is always useful to check visually the convergence by forming such plots Figure 4 Trajectories of 3 Markov chains for the first 3 parameter sampled at convergence over the last half million runs The 3 trajectories overlap on each panel and are

Pctiles all params png
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The true value and box summaries of the percentiles of the marginal posterior distribution of each parameter are shown in the next Figure Figure 6 Percentile plot 5th 25th 50th 75th and 95th percentiles of the posterior sample obtained for each parameter overlaid with their true value crosses We can see that

Yeast MCSIM png
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The two software give the same results with only rounding error differences Figure 2 Simulation of the time course of all model species with SBW 2 7 8 left and with GNU MCSim 5 3 0 right

J0 Kglc = f J0 Vmax png
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vector sampling to reach convergence component by component sampling was mixing very slowly Here is a plot of J0 Kglc versus J0 Vmax Figure 5 Correlation between J0 Kglc and J0 Vmax values sampled at convergence over the last half million runs The above correlation is quite bad news The estimates of the two

J0 Kglc = f J0 Vmax nice png
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posterior estimates of the 7 last parameters have not improved much but the additional experiment was not designed to do so The estimates of J0 Vmax and J0 Kglc are much better now Figure 9 Correlation between J0 Kglc and J0 Vmax values sampled at convergence over the last half million of the recalibration runs with additional data The positions of true values

J0 Kglc = f J0 Vmax population png
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everything has degraded The model has improved but not the results The estimates of J0 Vmax and J0 Kglc at the population leve are quite uncertain and higher than the true values Figure 10 Correlation between J0 Kglc and J0 Vmax values sampled at convergence over the last half million of the recalibration runs with additional data and a multilevel model True

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powrot

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img84 jpg 20 Jun 2003 12 08 46K img84 html 20 Jun 2003 12 08 625 img83 jpg 20 Jun 2003 12 08 55K img83 html 20 Jun 2003 12 08 625

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mcsim more options gif
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The Monte Carlo Advanced Options dialog allows a particular simulation to use special settings

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Correlations A C png
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Table gives the lower half of the correlation matrix of the 3000 parameter vectors sampled at convergence with only the the correlation coefficients higher than 0 1 in absolute value We can see a very strong correlation between J0 Vmax and J0 Kglc that is actually why we needed to perform vector sampling to reach convergence component by component sampling was

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Apr 20 2005 McSim moscow by McSim Home Studio Moscow

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Apr 20 2005 McSim moscow by McSim Home Studio Moscow