This was a semester project for a course on object-oriented programming. The task was to build program that could read in genetic information from two parent organisms and then create a variable number of offspring. Doing so required acquisition of domain knowledge (genetics) and an understanding of design patterns and the software development lifecycle.

The simulation creates an initial knowledge base from a definition file. That file contains descriptions of:

• an organism
• genes that organism can have
• two parents and the gene configurations which they are made of

external/instructor_files/ contains two sample definition files that you can use when running the program. If building from source, these files are copied to the build directory using CMake.

Reproduction mimics genetic processes closely, with a few simplifications. In src/core/, you will find models of components such as alleles, genes, chromosomes, and organisms. Organisms are composed of unpaired collections of chromosomes. This is slightly easier than the human case. From there, much is the same.

Chromosomes contain two strands on which genes are placed. During reproduction, the chromosomes of two parents are used to produce new chromosomes for an offspring organism. Much is left to chance. Certain complexities such as chromosomal crossover may occur. In that case, the alleles on a gene exchange during genetic recombination. The occurrence of crossover, as well as the variety of genes created, is printed in a final tally upon program exit.

Final development has been done using CMake 3.7 as the build system. There are two build targets of interest: genetics and tests. The former is the program itself and the latter builds the test suit. All tests were written using Google Test, which CMake will pull from the GitHub repository and build as part of the process.

cd into the cloned directory and run the following:

cmake .
make -j<# of threads to use>

This builds all projects. You can specify either genetics or tests to narrow compilation. E.g., make -j4 tests.

A new directory, build, should now exist in the root. It contains the target executables and two sample definition files.

Class documentation can be generated using Doxygen--a free tool that allows you to create Javadoc-style documentation for C++ source code. You can read more about Doxygen here.

Once installed, cd into the root directory of this project and run the doxygen command on the doxyconfig file:

doxygen doxyconfig

This will generate html (and latex) files and place them in docs/. Navigate to docs/html/index.html to get started.