Replace Jupyter NB with PY script to generate replicates and update README

[shachafl]

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README.md:36

• The description still refers to a 'Jupyter notebook' despite linking to a Python script; update the wording to accurately reflect that the tool is now a Python script.

We used our Jupyter notebook [Generate_replicates_for_network_inference.py](/CODE/Generate_replicates_for_network_inference.py) to call GeneNetWeaver to generate multiple replicates of steady-state and time-series gene expression datasets for realistic in silico networks of sizes of 50, and 100 genes containing various experimental conditions (knockouts, knockdowns, multifactorial perturbation, etc.).<br>

CODE/Generate_replicates_for_network_inference.py:60

• Using os.getcwd() here can be fragile if the working directory is not the expected simulation output folder; consider explicitly storing and referencing the simulation output directory.

for generated_file in os.listdir(os.getcwd()):