Arduino + flash no serial monitor

To start i'm sorry if this has been asked a thousand times already but i have searched the old information super highway for a while and have found no answer to it yet.

Basically i'm sending rfid tag id's to flash from my arduino board (uno) via tinkerproxy. It all works fine when i have the serial monitor open and then run the flash file but as soon as i just run the flash file nothing is sent to flash. Is there a way to get the code on the arduino board to run without me having to open up the serial monitor in the ide?

Cheers. (sorry if i'm being a proper noob)