Is there any simple build-in algorithm to obtain several "biological" replicates from one generated expression set (.pro) file.

Can SEED option be used for that?

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  1. No, the SEED parameter will change the randomized results, but not impose any biological connection between them. The simulation expresses genes and transcripts one-by-one according to the observed laws, but the program has no information about the functions of these genes that are in silico expressed and thus also not which cell type it is currently simulating. Currently, the only way to get that kind of information into the simulation is via the .pro file as you suggested.