Instructions for simulating the mu= 0.7, 1.0, 2.5 Growth rates from the paper.

COMPILING CODE

1) Code is located in /src directory
2) Make sure F95 flag in Makefile is set to the name of a fortran compiler installed on your computer
3) Type make to create the executable.

RUNNING THE SIMULATION

In essence, the growth rate is controled by the number of ribosomes in the simulation. This is set with the
-x flag on the command line which inputs the concentration of ribosomes in uM.
For the paper, mu=0.7 USED -x 12.5
               mu=1.0 USED -x 25.0
               mu=2.5 USED -x 100.0
Final time is fixed to 1000 seconds in the program
Note: mRNAs all have 5'/3' UTRs removed for simplicity since max initiation rate is assumed.
      This means start codon is @ nucleotides 1-3.

EXAMPLE OF RUNNING mu=0.7 SIMULATION

1) The /mu-0.7 /mu-1.0 and /mu-2.5 directories contain the cellular mRNA data files needed to run the simulation.
2) Example: mu = 0.7
   a) In the /mu-0.7 directory, the mRNA-T07.dat file contains 650 lines of sequence information, which is the T07
      transcriptome used in the paper.
   b) To run this simulation, on the command line type:
      ./Prosyn.x -x 12.5 -s mRNA-T07.dat
      This will start the run using ~7500 ribosomes and read in the mRNA-T07.dat file for the transcritpome information.
      Other cellular proteins and tRNAs will be fixed by a ratio to the total ribosome number.

OUTPUTED FILES

1) ribo_subunits.dat => The 30SPIC pathway intermediates and 30S and 50S.
2) init_factors.dat  => The initiation factor numbers with IF2:GDP (IF2-2) and IF2:GTP (IF2-3)
3) recy_factors.dat  => The recycling factor numbers with RF3:GDP (RF3-2) and RF3:GTP (RF3-3)
4) elong_factors.dat => The elongation factors numbers (EfTu/EfTs/EfG) in complex w/wo GTP/GDP
5) ribo_dependent_pro.dat => Numbers of proteins which can bind to mRNA/ribosomes (30S:PIC,TC,etc)
6) ribo_stats.dat    => The numbers of ribosomes in different states (70S:IC,70S:EC,70S:RC,stalled)
7) pro-gtp_consumption.dat => This lists the number of IF2:GTP, Ternary Complex, EFG:GTP, etc
   that have been "consumed" by ribosomes. The finaly two numbers list number of premature termination
   events and the total number of proteins produced.
8) tRNA-free.dat => The number of each tRNAs (free) are listed by their recogntion codon tRNA 1=aaa 2=aac 3=aag 4=aau
9) tRNA-tcx.dat  => The number of each tRNAs (in complex as TC)
10) elon.time    => The total elongation time for each ribosome.
                    First column is the current time in the simulation
                    Second column is the total elongation time
                    Third column is the length of the reading frame in nt
                    Fourth Column is the Cp value for this elongation event.
11) post.time    => Length of time to move from preHC to 70S:RC
                    First column is the current time in the simulation
                    Second column is the total time to mature into 70S:RC
                    Third column is the length of the reading frame in nt
                    Fourth Column is the RF3 recycling pathway type.
12) init.time    => Length of time to move from 30S:IC to 70S:EC complex
                    First column is the current time in the simulation
                    Second column is the total initiation time
                    Third column is the nucleotide number of location of the P-Site of the next downstream ribosome
13) term.time    => Length of time to split ribosome.
                    First column is the current time in the simulation
                    Second column is the total time to split the ribosome
                    Third column is the distance (in nucleotides) to the P-site of upstream ribosome
                    Fourth Column is the recycling factor used (RF1=1,RF2=2).
