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"

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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