In your article, I became particularly interested in the SERGIO simulator, which can simulate approximate real-world datasets based on a given gene regulatory network (GRN). However, I have come across a situation where the simulator fails to simulate when there are feedback regulations within the GRN (where the expression of gene S is activated by gene T, and the expression of gene T is inhibited by gene S). I am curious to know how to appropriately set the corresponding values for "Input_filetargets = Interaction.txt" and "Input_filereges = Reges.txt" in the context of the GRN with feedback regulation.
I would greatly appreciate it if you could spare some time from your busy schedule to discuss this problem with me. Your expertise and guidance in addressing this issue would be immensely valuable, and I am eager to learn from you.
Thank you very much for your attention and consideration. I look forward to your response.
Dear Professor Payam Dibaeinia,
In your article, I became particularly interested in the SERGIO simulator, which can simulate approximate real-world datasets based on a given gene regulatory network (GRN). However, I have come across a situation where the simulator fails to simulate when there are feedback regulations within the GRN (where the expression of gene S is activated by gene T, and the expression of gene T is inhibited by gene S). I am curious to know how to appropriately set the corresponding values for "Input_filetargets = Interaction.txt" and "Input_filereges = Reges.txt" in the context of the GRN with feedback regulation.
I would greatly appreciate it if you could spare some time from your busy schedule to discuss this problem with me. Your expertise and guidance in addressing this issue would be immensely valuable, and I am eager to learn from you.
Thank you very much for your attention and consideration. I look forward to your response.
Thanks and regards.