Example Notebook Problems

[WilliamIX]

Found some problems with example notebooks. Making a list here:

1. In Notebook 1 (CRNs) the text doesn't quite match the code for the new way propensities work.
2. Notebook 4 (Gene Regulation) Example 4 (Regulated Promoter) is not working correctly for some reason. Probably the parameter values?

[zoltuz]

Suggestion for the first notebook:

• Point out the colon notation for complexes (add reference: BFS chapter 2)
• Explain that A + C <-> E -> D is the same as A + C <-> E and E -> D (for beginners)

[zoltuz]

typo in the markdown cell "Non-massaction propensities in BioCRNpyler": propritional species -> proportional species
https://github.com/BuildACell/BioCRNPyler/blob/master/examples/1.%20Building%20CRNs%20Directly.ipynb

[WilliamIX]

At the end of this process, read through all the example notebooks and check for consistency, clarity, etc.

[WilliamIX]

Dilution listed as part of TxTlExtract in the Transcription / Translation notebook.