To run the notebook for this post in version 12.0 of Mathematica make the following changes:

1) Replace the first input

<<CompartmentalModeling`

with

Get@CloudObject["https://www.wolframcloud.com/obj/rnachbar/Published/CompartmentalModeling.wl"]

2) Replace all instances of stochasticSolve with StochasticSolve

3) Don't evaluate the input in the section "Simulation loop"

The stochastic simulation is not running properly because it's trying to use the CreateDataStructure function which is not in version 12.0.

Let me see what it takes to run the notebook in version 12.0, and then send you either a short list of changes, or a new notebook. I might not be able to get to this until Wednesday, however.

Really Thanks for your helpful. But there are some problem as In[79]:= {times, states} = Transpose@Normal@stateList; states = Transpose@states;

During evaluation of In[79]:= Set::shape: Lists {times,states} and Transpose[CreateDataStructure[DynamicArray]] are not the same shape.

During evaluation of In[79]:= $RecursionLimit::reclim2: Recursion depth of 1024 exceeded during evaluation of Transpose[states].

Next, we compute InterpolatingFunction objects for each variable. Note that runs of constant state are replaced by just the first instance, and that we use an interpolation order of 0.

In[81]:= soln = First@{Thread[ vars -> (Interpolation[ Join @@ Replace[ SplitBy[Thread[{times, #}], Last], {a, _, z} :> {a}, {1}], InterpolationOrder -> 0] & /@ states)]}

During evaluation of In[81]:= $RecursionLimit::reclim2: Recursion depth of 1024 exceeded during evaluation of Transpose[states].

Out[81]= Hold[soln = First[{Thread[ vars -> (Interpolation[ Join @@ Replace[ SplitBy[Thread[{times, #1}], Last], {a, _, z} :> {a}, {1}], InterpolationOrder -> 0] &) /@ states]}]]

First I 'd like to thank you for you kind reply. Really I have version 12. How can I fix the problem in version 12 ?

Please I have the following error while evaluating you notebook

In[369]:= SeedRandom[1425367]
solnsCME = 
   Table[stochasticSolve[modelData["Rates"] /. paramsN, 
     modelData["StoichiometricMatrix"], 
     Through@modelData["Variables"][0] /. Rule @@@ inits /. paramsN, 
     modelData["Variables"], {t, 0, tmax}], 500]; // Timing

During evaluation of In[369]:= Set::shape: Lists {times$25658,states$25658} and Transpose[CreateDataStructure[DynamicArray]] are not the same shape.

During evaluation of In[369]:= $RecursionLimit::reclim2: Recursion depth of 1024 exceeded during evaluation of Transpose[states$25658].

During evaluation of In[369]:= $RecursionLimit::reclim2: Recursion depth of 1024 exceeded during evaluation of Transpose[states$25658].

During evaluation of In[369]:= Set::shape: Lists {times$25667,states$25667} and Transpose[CreateDataStructure[DynamicArray]] are not the same shape.

During evaluation of In[369]:= $RecursionLimit::reclim2: Recursion depth of 1024 exceeded during evaluation of Transpose[states$25667].

During evaluation of In[369]:= General::stop: Further output of $RecursionLimit::reclim2 will be suppressed during this calculation.

During evaluation of In[369]:= Set::shape: Lists {times$25682,states$25682} and Transpose[CreateDataStructure[DynamicArray]] are not the same shape.

During evaluation of In[369]:= General::stop: Further output of Set::shape will be suppressed during this calculation.

Out[370]= {78.5, Null}

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