To compile the program type on the command line:
./compile.sh
To run the program type:
./run.sh params/params_default.txt
This will start the simulation model with the parameters as specified in the sample params_default.txt parameter file.
Running the program without specifying a parameter file will result in a simulation with randomly generated transcriptome.
The directory "biodata" contains sample data to run a simulation of translation for Saccharomyces cerevisiae in rich medium. The files are as follows:
YeastGenesFasta.txt: A description of all ORFs in Fasta format
yeast_codon_abundance.csv: This file determines the cognate/non-cognate tRNA and their abundance.
5UTRs_mRNA_levles_and_synth_rates.csv: A description of the availability of the mRNA numbers and the affinities of ribosomes to the individual mRNA species.
OUTPUT:
In addition to comprehensive summaries about various statistics of the simulation that will be generated in the "results" directory the program also produces continuous output to stdout. This output is of the form: YDR461W 38 0.023846066686404207 7.651532849886225 7.627686783199821 0.20072859955789002 3 0.931215 YJL189W 53 5.466124486264808E-4 7.859910793096623 7.859364180647996 0.1482898902009056 5 0.930295 YLR388W 58 6.057721033941735E-4 8.68113756951113 8.680531797407735 0.14966434133461612 3 0.926805 YDL232W 38 0.016721052762241968 8.703983987477855 8.687262934715614 0.22861218249251616 3 0.926745 YOR302W 27 0.03492805778475045 9.446525654885459 9.411597597100709 0.34857768878150774 2 0.923575 The first entry is the standard name of the ORF, its length, the time when the last translation round has started [in seconds since starting of the model], when it has ended [in seconds since starting the model], the total time taken to translate one round [in seconds], the average time to translate one codon of this ORF [in seconds], the number of ribosomes attached to this ORF at the current time, and the proportion of free ribosomes to all ribosomes. If the last number is zero, this means that no ribosomes are available.