# rvencio jul-08-2014
#
# to run simulation just change parameters and copy-paste the code below into your R section

# model parameters
	t_stall = c(30, 50, 80) # time spent stalled (units of time)
	t_iti = 10 # intrinsic transcription initiation interval (unit of time)
	x_stall = c(35, 40, 55) # position where pausing site(s) ir(are) (bp)
	t_atabase = 1 # normal (non-paused) time spent at each base transcribing (units of time)
	L = 1000 # gene length (bp)

# simulation parameters
	T = 1E5 # total simulation time

#starting simulation

		DNAtime = rep(t_atabase, L) # all bases along gene hold RNApol for the same amount of time
		DNAtime[x_stall] = t_stall  # except at these positions where RNApol pauses longer times
		transcript = NULL # inicialization of list of transcripts produced

		t = 1 # clock ticks for the 1st time with the 1st RNApol to arrive
		polx = 1 # the 1st RNApol to arrive starts at genomic position x=1
		polt = 1 # the 1st RNApol to arrive already spent 1 time unit at arriving position

		while(t < T){ # simulation goes on until time is up
			if(t %% t_iti == 0){ # a new RNApol must arrive and start new transcript if it is time
				if(all(polx != 1)){ # ... but only if there is no other RNApol at position x=1 
					polx = c(polx, 1) # start a new RNApol at x=1
					polt = c(polt, 0) # start timer for this new RNApol
				}
			}

			if(length(polx) == 0){ break } # no RNApols, nothing to do, finish simulation

			for(i in length(polx):1){ # update every single RNApol available to new status
				if(polt[i] >= DNAtime[polx[i]]){ # is it time to leave current position?
					if(any(polx[i]+1 == polx)){ # if next base occupied then
						transcript = c(transcript, polx[i]) # release transcript up to here
						polx = polx[-i] # release this RNApol from DNA and from our list
						polt = polt[-i] # release this RNApol from DNA and from our list
					}else{ # if next position is available
						if(polx[i] + 1 > L){ # if next position is outside gene
							transcript = c(transcript, polx[i]) # transcript is over
							polx = polx[-i] # release RNApol from our list
							polt = polt[-i] # her job is over
						}else{ # if next position is valid
							polx[i] = polx[i] + 1 # move RNApol fwd
							polt[i] = 1 # and wait there for another time unit 
						}
					}
				}else{ # if it is not time to leave current position
					polt[i] = polt[i] + 1 # just wait there for another time unit 
				}
			}
			t = t + 1 # clock ticks
		}

#end of simulation


# save the number of molecules transcribed by all RNApol depending on transcript size
		output = table(transcript)

# show output at your screen
		print(output)