LES - Lineage Evolution System

 Downloads

Main program

• LES.jar   328 KB   (All platforms, Java™ 1.4 or greater required)

Data sets

• pma.alm   20 KB   Pellioditis marina cell lineage (data from Houthoofd et al., 2003)

 Usage

To execute the program open a command line, change to the directory where you saved the LES.jar file and type:

    java -jar LES.jar [options]

where [options] are:

    -seedfile <File>     - File with initial parent lineage [Default seed.alm]
    -randomseed          - Create a random seed lineage [Default false]
    -start <int>         - Generation at which to start experiment [Default 1]
    -generations <int>   - No. generations in experiment [Default 5]
    -period <int>        - Generation period for saving files [Default 1]
    -threads <int>       - No. threads generating offspring [Default 1]
    -offspring <int>     - No. offsprings per thread per generation [Default 10]
    -exclude             - Exclude parent lineage from selection [Default false]
    -swaps <int>         - No. pairs of nodes/cells to swap [Default 1]
    -fitness <text>      - Fitness function coefficients ("RR^j (D|D'+1)^k Depth^l")
                           [Default "1 0 0"]
    -gradual             - Use gradual spatial constraint (D') [Default true]
    -decplaces <int>     - No. decimal places for output [Default 5]
    -verbose             - Output runtime information to console [Default false]

Example

To run the simulation on Fig. 4b (green) use the command (on one line):

    java -jar LES.jar -seedfile pma.alm -generations 50000 -offspring 100
         -fitness "1 1 0" -period 5000