- Simulate sequence variants in pool of a wild type sequence (random mutagenesis)
- Randomly assign fitness values for each position-wise mutation and pairwise epistatic effects
- Derive species frequencies in equilibrium
- Add statistical noise
- Output positionwise mutant counts and the groundtruth
Detailed explanation will be added
Go into the MIMESim directory and create a build directory and cmake and make from there.
cd /path/to/MIMESim
mkdir build
cd build
cmake ..
make
This will create the binary file .../MIMESim/build/bin/MIMESim_prog
Running the program with an optional parameter, giving the path to the result directory. If no parameter is given, the output will be written to the newly created directory ../results.
/path/to/MIMESim_prog [result_directory]
If no parameter file is present in the given result directory (or no directory was given at all), the programm will run the simulation with default paraters (tba). After the run it will create the parameter file in the result directory together with the other output.
If you want to set the simulation parameters, create the parameters.txt file in the desired result directory and add the following parameter names and values (tab separated):
| parameter | type | description |
|---|---|---|
| kd_wt | (float) | (absolute Kd for the wildtype sequence (default: 1)) |
| p_effect | (float) | probability per position to have an effect on function when mutated (default: 0.5) |
| p_epistasis | (float) | probability for each pair of mutations to have epistatic effect (default: 0.3) |
| L | (int) | Length of the sequence (default: 50) |
| q | (int) | (number of possible symbols per position (default: 2)) |
| M | (int) | (size of initial population (default: 12000000) |
| p_mut | (float) | probability for each position of being mutated (default: 0.1) |
| p_error | (float) | probability of introducing an error (default: 0.01) |
Comments:
- Right now, kd_wt is always 1 and also M is always 12 mio, but this can be easily adjusted in the code.
- It is only working for q=2 atm.
- B_tot = total protein concentration is not in the parameter setting right now. The amount of protein is given in relation to the amount of sequences, and is set to 2.0