Documentation for ctRSD-simulator-2.0 can be found here:

https://ctrsd-simulator.readthedocs.io/en/latest/

The 2022 Science Advances manuscript folder contains an outdated version of the simulator used in that publication

The 2023 ACS Synthetic Biology manuscript folder contains the version of the v2.0 simulator used in that publication

The ctRSD-simulator-2.0 folder contains the latest version of the simulator. v2.0 is not compatible with the nomenclature used in v1.0 but all the examples for v1.0 have been reimplemented with v2.0 and uploaded in Examples.