flyOpt {#mainpage}

flyOpt is a combined simulator and optimizer of D. melanogaster gap gene network. Simulator implements the Connectionist Model of Development in which the interaction between group of genes being simulated both in time and space (embryo) to produce spatio-temporal gene expression patterns of gap genes. The optimizer embedded in the code uses Scatter Search algorithm to find parameters of the gap genes network by fitting the model to the data.

Requirements

Before compilation, you need to install several key packages:

• GSL
• Sundials
• gnuplot, only for visualization, v script visualizer/
• Perl, necessary dependency of flyOpt code. (Perl is usually available on macOS (OS X) and almost all Linux system.)
• Doxygen, for documentation

The packages listed above can be install using homebrew on macOS by: brew install gsl sundials gnuplot doxygen. On Linux, search for the packages in your package manager.

Components and Structure of the Code

The code consists of few components:

• D. melanogaster gap gene network simulator (fly/ & utils/)
• Scatter Search optimization algorithm (ss/)
• Enhanced Scatter Search optimization algorithm (ess/)
• Visualization scripts, a simple Perl script implemented to read parameters from an input file, simulate the expression patterns and plot the final results. (visualizer/)

Compiling and Running the code

Setting the Makefile parameters

Before starting the compilation process you need to make sure that fly/Makefile knows sundials and gsl path in your system. Set SUNDIAL variable at line 57 to your sundial installation path. In most cases system can find GSL if it's installed properly.

Compilation

The compilation process is based on the optimization method of choice. Compilations with the METHOD=-DSS generated the fly_ss executable which optimize the problem using Scatter Search algorithm.

make veryclean; make METHOD=-DSS deps; make METHOD=-DSS

Compilation with the flag METHOD=-DESS produces the fly_ess executable which optimize the problem using Enhanced Scatter Search algorithm.

make veryclean; make METHOD=-DESS deps; make METHOD=-DESS

Running the Simulation

There are several options available via command line to run the optimizer. Almost all the command line parameters are also available on the input file as well. In order to get the list of parameters run: ./fly_[method] -h to get:

Usage: fly_[method] [options] <datafile>

Argument:
  <datafile>          input data file

Options:
  -a <accuracy>       solver accuracy for adaptive stepsize ODE solvers
  -D                  debugging mode, prints all kinds of debugging info
  -f <param_prec>     float precision of parameters is <param_prec>
  -g <g(u)>           chooses g(u): e = exp, h = hvs, s = sqrt, t = tanh
  -h                  prints this help message
  -i <stepsize>       sets ODE solver stepsize (in minutes)
  -m <score_method>   w = wls, o=ols score calculation method
  -n                  nofile: don't print .log or .state files
  -N                  generates landscape to .landscape file in equilibrate mode 
  -s <solver>         choose ODE solver
  -v                  print version and compilation date
  -w <out_file>       write output to <out_file> instead of <datafile>
  -y <log_freq>       write log every <log_freq> * tau moves

Sample run command would be like:

./fly/fly_ss -s rck -i 4.0 -a 0.001 input/sample_input.inp

The results of the simulation will be saved in a new folder at input/sample_input.inp/.

Note: Make sure that input file contain appropriate algorithm parameters. Check [$ss paramters](ss/README.md) and [$ess paramters](ess/README.md)

Visualization

In order to visualize the simulation results, you can run drawPlots script. drawPlots uses v script to simulate and plot the gene expression levels in all predefined time-points (10.550, 24.225, 30.475, 36.725, 42.975, 49.225, 55.475, 61.725, 67.975). For more detailed visualization check v -h.

./drawPlots output_file

Note:: Make sure that $unf and $printsc variables at line 59 of v script points to unfold and printscore executable.

Documentation

For full documentation, run doxygen command in the main folder. Then open doc/html/index.html